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- PDB-7zra: Crystal structure of E.coli LexA in complex with nanobody NbSOS1(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zra | ||||||
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Title | Crystal structure of E.coli LexA in complex with nanobody NbSOS1(Nb14497) | ||||||
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![]() | TRANSCRIPTION / Transcriptional repressor DNA binding autoproteolysis Nanobodies | ||||||
Function / homology | ![]() repressor LexA / SOS response / DNA replication / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maso, L. / Vascon, F. / Chinellato, M. / Pardon, E. / Steyaert, J. / Angelini, A. / Tondi, D. / Cendron, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway. Authors: Maso, L. / Vascon, F. / Chinellato, M. / Goormaghtigh, F. / Bellio, P. / Campagnaro, E. / Van Melderen, L. / Ruzzene, M. / Pardon, E. / Angelini, A. / Celenza, G. / Steyaert, J. / Tondi, D. / Cendron, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 212.4 KB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7b5gC ![]() 7ocjC ![]() 1jhcS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22388.713 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminus is not visible in the electron density maps. Source: (gene. exp.) ![]() ![]() Gene: lexA_1, lexA, lexA_2, lexA_3, lexA_4, lexA_5, lexA_6, A6581_03840, A6592_09000, A6V01_14725, A8C65_05740, A9819_23115, A9P13_24790, A9R57_24265, A9X72_23540, AAW05_04940, AC067_05020, AC789_ ...Gene: lexA_1, lexA, lexA_2, lexA_3, lexA_4, lexA_5, lexA_6, A6581_03840, A6592_09000, A6V01_14725, A8C65_05740, A9819_23115, A9P13_24790, A9R57_24265, A9X72_23540, AAW05_04940, AC067_05020, AC789_1c44530, ACN002_4144, ACN68_15885, ACN81_05765, ACU57_23725, ACU90_04800, AJ318_13980, AM270_18420, AM446_25905, AM464_13585, AM465_02855, AMK83_25365, AML07_00445, AML35_16500, APT94_01725, APU18_20100, APZ14_12275, ARC77_17360, AU473_00505, AUQ13_09675, AUS26_09870, AW059_18350, AW106_02825, AWB10_24615, AWE53_003010, AWF59_006810, AWG78_010890, AWG90_025185, AWP75_14755, AZZ83_003567, B6V57_23175, B7C53_16050, B9M99_07260, B9N33_14930, B9T59_11225, BANRA_02722, BANRA_02895, BANRA_05124, BB545_04745, BE963_11630, BEN53_25180, BER14_12995, BFD68_07790, BHF03_13425, BHF46_15090, BHJ80_01810, BHS81_24295, BHS87_22640, BIQ87_23185, BIU72_20655, BIZ41_02125, BJJ90_24770, BK248_24315, BK292_01025, BK296_23860, BK334_08815, BK373_03960, BK375_08450, BK383_21615, BMA87_07675, BMT49_20690, BMT91_12915, BN17_40181, BOH76_06090, BON63_06530, BON65_23060, BON66_03315, BON69_22095, BON71_16410, BON75_07080, BON76_04855, BON83_16235, BON86_25705, BON87_02545, BON91_12300, BON92_17725, BON94_08075, BON95_04860, BON96_03145, BON98_14025, BTQ04_27960, BTQ06_28255, BUE81_22465, BvCms12BK_04297, BvCms2454_00415, BvCms28BK_01342, BvCms35BK_01831, BvCmsC61A_01832, BvCmsHHP001_00842, BvCmsHHP019_03449, BvCmsHHP056_02653, BvCmsKKP036_01653, BvCmsKKP061_03212, BvCmsKSNP073_04428, BvCmsKSNP081_02209, BvCmsKSNP120_00016, BvCmsKSP011_01869, BvCmsKSP024_01390, BvCmsKSP026_03995, BvCmsKSP045_02606, BvCmsKSP058_01651, BvCmsKSP067_03973, BvCmsKSP076_00063, BvCmsNSNP036_01892, BvCmsNSP006_05193, BvCmsNSP007_02439, BvCmsNSP047_02150, BvCmsNSP072_02985, BvCmsOUP014_01488, BvCmsSINP011_01581, BvCmsSINP022_02516, BvCmsSIP019_02982, BvCmsSIP044_03653, BVL39_05000, BW690_17275, BWI89_17045, BWP17_09115, BXT93_20190, BZL31_27495, BZL69_04975, C2M16_18650, C2U48_12390, C4K41_22540, C4M78_06355, C5715_10070, C5F72_25480, C5F73_24600, C5N07_20195, C5P01_10950, C5P44_17630, C6669_07275, C6B13_20680, C7235_23375, C7B02_13860, C7B06_21440, C7B07_20950, C7B08_17115, C7B18_19350, C9098_11905, C9114_00185, C9141_04535, C9160_08095, C9162_23740, C9201_06385, C9306_11555, C9E25_05905, C9E67_28315, C9Z03_09215, C9Z23_10210, C9Z28_18985, C9Z29_15625, C9Z37_11110, C9Z39_12685, C9Z43_13055, C9Z68_12230, C9Z69_10275, C9Z70_15630, C9Z78_21525, C9Z89_05965, CA593_05680, CCZ14_07840, CDC27_21910, CDL37_20795, CF006_04145, CG692_11650, CI641_013760, CI693_02120, CI694_23155, CIG45_19390, CJU63_23870, CJU64_24205, CMR93_13445, CO706_19840, COD30_15395, COD46_18700, CQP61_25715, CR538_23835, CR539_02040, CRD98_27320, CRE06_21195, CRJUMX01_510039, CRM83_18295, CRT43_24270, CRX46_18555, CSB64_02010, CT146_24150, CUB99_11400, CV83915_01994, CVH05_06385, CWM24_08770, CWS33_15975, D0X26_12200, D1912_18705, D2184_21525, D2185_07080, D2188_17815, D3821_04640, D3822_08745, D3M98_15580, D3O91_19225, D3P01_12220, D3P02_10990, D4011_20000, D4023_17595, D4074_20080, D4628_12380, D4636_09720, D4638_24525, D4660_19160, D4718_13325, D4L91_18735, D4M06_19695, D4M76_10435, D4U49_11220, D4U85_19640, D4V08_08845, D5H35_01910, D5I97_18270, D6004_01850, D6C36_19740, D6D43_19725, D6T60_08900, D6T98_07050, D6W00_08775, D6X36_02250, D6X63_25780, D6X76_22790, D7K33_19360, D7K63_02835, D7K66_21305, D7W70_12300, D7Y10_01185, D7Z75_09495, D8Y65_18220, D9610_00735, D9C99_09310, D9D20_17210, D9D33_01860, D9D43_18385, D9D44_06445, D9D94_04730, D9E13_11180, D9E19_14095, D9E34_02075, D9E35_10415, D9E49_22250, D9E73_19440, D9F17_19275, D9F32_11525, D9F87_12490, D9G11_22460, D9G29_18660, D9G42_14820, D9G48_15290, D9G69_15475, D9G95_21630, D9H10_15220, D9H36_09830, D9H53_20975, D9H68_20260, D9H70_15350, D9H94_14230, D9I18_21060, D9I20_19240, D9I87_21035, D9I88_03895, D9I97_23010, D9J03_04410, D9J11_07590, D9J44_17675, D9J46_13285, D9J52_18345, D9J58_14965, D9J60_05135, D9J63_12310, D9J78_21390, D9K02_09285, D9K48_05710, D9K54_02940, D9L89_19960, D9L99_05045, D9S45_16730, D9X77_17715, D9X97_19985, D9Z28_19505, DAH18_17020, DAH26_23105, DAH30_16750, DAH32_05100, DAH34_09745, DAH37_23000, DAH43_08050, DB359_22770, DBQ99_24230, DD762_09570, DEN86_01240, DEN89_16940, DEN97_12815, DEO04_14355, DEO19_12485, DEO20_13045, DIV22_28315, DJ487_17695, DJ503_03205, DK132_10450, DL251_19160, DL257_06320, DL292_14670, DL326_18360, DL455_17780, DL479_04890, DL530_02190, DL545_23320, DL705_06290, DL800_28030, DL979_22465, DLT82_16100, DLU50_04305, DLU67_12520, DLU82_06835, DLW60_00780, DLW88_15040, DLX38_07225, DLX40_14200, DLY41_09575, DLY44_12300, DM102_07955, DM129_07275, DM155_00780, DM267_22275, DM272_08145, DM280_16450, DM296_05455, DM382_06365, DM820_11410, DM962_16745, DM973_17240, DMI04_18725, DMI53_18525, DMO02_19335, DMY83_08280, DMZ50_11405, DN627_13770, DN660_12190, DN700_09495, DN703_20325, DN808_20920, DNB37_17705, DNC98_13900, DND16_08380, DND79_11485, DNI21_02325, DNJ62_19610, DNK12_18155, DNQ45_03405, DNR35_06920, DNR41_16590, DNW42_02895, DNX19_05225, DOE35_19020, DOM23_10665, DOS18_18880, DOT81_19955, DOU81_18220, DOY22_18350, DOY56_18570, DOY61_11305, DOY67_06200, DP258_12750, DP265_01880, DP277_17730, DQE91_14650, DQF36_19215, DQF57_12540, DQF71_02370, DQF72_01950, DQG35_19915, DQO13_07445, DQP61_07285, DRP48_19990, DRW19_10040, DS143_02030, DS721_17960, DS732_01915, DS966_07340, DT034_16995, DTL43_19530, DTL90_18345, DTM10_17250, DTM45_22000, DTZ20_07940, DU309_08590, DU321_20700, DU333_20915, DVB38_00780, DW236_20350, DWB25_23105, DXT69_11240, DXT71_13455, DXT73_06680, DXX80_014420, E0I42_01715, E0K84_14705, E0L04_06555, E0L12_12475, E2112_13635, E2119_15925, E2127_04695, E2128_24955, E2129_11665, E2134_19225, E2135_15890, E2148_17730, E2855_05069, E2863_04868, E4A44_08405, E4K51_08400, E4K55_09280, E4K59_02705, E4K60_21225, E4K61_06350, E5P22_21020, E5P24_22750, E5P28_22440, E5P37_19690, E5S42_14590, E5S56_16625, E5S58_10005, E5S61_13810, E5S62_09140, EA159_09860, EA164_11895, EA167_12330, EA174_06160, EA184_14750, EA189_16420, EA191_11120, EA198_19920, EA200_15705, EA203_12170, EA213_12715, EA214_12670, EA218_06700, EA222_18665, EA223_05425, EA225_15150, EA231_21330, EA232_11815, EA233_13540, EA235_13150, EA239_14350, EA242_15215, EA245_21190, EA247_19925, EA250_22905, EA410_10735, EA429_14660, EA433_09295, EA434_07730, EA435_14070, EA834_14185, EAI42_11775, EAI46_13910, EAI52_14305, EAM59_19660, EAN70_04295, EAN77_18045, EAX79_14320, EB476_06510, EB509_23270, EB510_19485, EB515_21475, EB525_RS22295, EBA46_21785, EBA84_21540, EBJ06_20090, EBM08_00725, EC1094V2_4222, EC3234A_77c00360, EC3426_00367, EC382_06195, EC95NR1_03586, ECONIH1_23895, ECs5026, ECTO124_04687, ECTO6_04452, ED178_02160, ED225_20150, ED307_20800, ED600_11955, ED607_20180, ED611_21565, ED648_10135, ED903_21355, ED944_20920, EEA45_23665, EEP23_23665, EF082_14250, EF173_02775, EG075_18135, EG599_11110, EG796_08865, EG808_11410, EGC26_22390, EGT48_16960, EGU87_16570, EH186_18415, EH412_04435, EHD45_05640, EHD63_19000, EHD79_12175, EHH55_01035, EHJ36_05660, EHJ66_21070, EHV81_14020, EHV90_14340, EHW09_21540, EHX09_18295, EI021_16120, EI028_05870, EI032_15785, EI041_04290, EIA08_19795, EIA21_16610, EIZ93_23270, EJ366_21585, EJC75_19935, EKI52_13610, EL75_4145, EL79_4350, EL80_4257, ELT17_04335, ELT20_15125, ELT22_19765, ELT23_17595, ELT33_14365, ELT48_13885, ELT49_00210, ELT58_16885, ELU82_17295, ELU85_16290, ELU96_14010, ELV00_20075, ELV05_04290, ELV08_22365, ELV13_10080, ELV15_24385, ELV22_20245, ELV24_10490, ELV28_08325, ELX56_12745, ELX70_12445, ELX76_18040, ELX79_01350, ELX83_19330, ELY05_20415, ELY23_17950, ELY24_02305, ELY41_24075, ELY48_01785, ELY50_17875, EO241_22225, EPS91_05510, EPS94_15340, EPU41_22875, EQ820_09870, EQ823_07865, EQ825_11565, EQ830_09950, EQO00_24610, ERL57_14825, ERS085365_02976, ERS085366_03456, ERS085374_01624, ERS085379_03983, ERS085383_01448, ERS085386_02660, ERS085404_01243, ERS085406_04198, ERS085411_04446, ERS085416_00631, ERS139211_04672, ERS150873_01187, ERS150876_04135, EST51_23545, EVY14_11520, EWK56_09425, EXM29_06605, ExPECSC019_02605, ExPECSC038_04549, ExPECSC065_01920, EXX06_18435, EXX13_12090, EXX23_19315, EXX24_09955, EXX53_09260, EXX55_18970, EXX71_07865, EXX78_13230, EXX87_20000, EYD11_21280, EYX82_05305, EYX99_01640, EYY27_19365, EYY34_21065, EYY78_21440, F1E13_08855, F1E19_14155, F7F00_04830, F7F11_03715, F7F18_10310, F7F23_02515, F7F26_18655, F7F29_21255, F7F56_09730, F7G01_19665, F7G03_07710, F9040_10620, F9050_18985, F9225_08300, F9B07_06640, F9X20_06245, F9Z53_12245, F9Z74_02500, FAF34_027445, FE846_20710, FKO60_19090, FNJ67_24760, FNJ69_19430, FNJ83_25115, FORC82_4459, FPI65_24840, FQ021_13785, FQ022_13220, FQ915_20070, FQR64_21510, FQU83_25315, FQZ46_11420, FRV13_15940, FTV92_16270, FTV93_16625, FV293_00180, FV295_14155, FV438_02950, FVB16_13290, FY127_04780, FZ043_01435, FZC17_04895, FZN06_07660, FZN26_04905, FZN30_09565, G3565_23685, G3V64_10445, G5603_20840, G5608_21780, G5616_05135, G5632_08040, G5668_16270, G5670_04760, G5675_07615, G5680_02920, G5686_19405, G5688_11635, G5696_16625, G5697_10455, GFU40_20155, GFU45_18365, GFU47_11010, GHR40_03285, GII67_18535, GII91_01590, GIJ01_07080, GIY13_22705, GIY19_15100, GJ11_25525, GJ638_08800, GJD97_25670, GKE15_08795, GKE16_10270, GKE22_09815, GKE24_10940, GKE26_10295, GKE29_07830, GKE31_09080, GKE39_08675, GKE46_08475, GKE53_08285, GKE58_08305, GKE60_08375, GKE64_08350, GKE69_08185, GKE77_10555, GKE79_08190, GKE87_03580, GKE92_11980, GKE93_09555, GKE98_17470, GKF00_11225, GKF03_07640, GKF21_19525, GKF28_19545, GKF34_19920, GKF39_10130, GKF47_19635, GKF52_19185, GKF74_07005, GKF86_09530, GKF89_08240, GKG08_19925, GKG09_19795, GKG11_19965, GKG12_13240, GKG22_19630, GKG29_19840, GN312_11355, GNZ00_12570, GNZ02_08260, GNZ03_05545, GNZ05_23055, GP650_09375, GP654_14900, GP661_10840, GP662_05880, GP664_12905, GP666_14410, GP671_00680, GP678_14315, GP689_08955, GP698_02940, GP700_05045, GP711_15355, GP712_07365, GP720_18065, GP727_20045, GP892_04865, GP912_08340, GP935_16255, GP945_10980, GP946_12270, GP950_01700, GQA23_07565, GQA63_11350, GQA64_11565, GQE22_22480, GQE30_09515, GQE33_21095, GQE34_18985, GQE36_21390, GQE42_17480, GQE47_16615, GQE51_19030, GQE58_14030, GQE64_15035, GQE68_09185, GQE87_13955, GQE88_20795, GQE93_06065, GQF59_13075, GQL64_02840, GQM04_21825, GQM06_05485, GQM09_07375, GQM10_00185, GQM13_10075, GQM17_17755, GQM18_21055, GQM28_14230, GQN16_10665, GQN24_10350, GQN33_15605, GQS26_13850, GQY14_18825, GRW05_25935, GRW12_07495, GRW27_03680, GRW30_10035, GRW42_18565, GRW57_21705, GRW80_00680, GRW81_20425, GUB08_14505, GUB85_10045, GUB91_12015, GUB95_13125, GUC01_08305, GUC12_14155, GUC40_13020, GUI16_13780, GUI33_07450, GZS12_22285, HmCms169_03196, HmCms184_01443, HmCmsJML074_03763, HmCmsJML079_02438, HmCmsJML146_04299, HmCmsJML204_02607, HmCmsJML236_03697, HMPREF3040_01362, HW43_01890, MJ49_09110, MS6198_46970, MS8345_04507, NCTC10082_02015, NCTC10089_04675, NCTC10090_02705, NCTC10764_02888, NCTC10766_00857, NCTC10767_00646, NCTC10963_04726, NCTC10974_05266, NCTC11022_04367, NCTC11126_02097, NCTC11181_01887, NCTC11341_02866, NCTC12650_04928, NCTC12950_05138, NCTC13127_06081, NCTC13216_02170, NCTC13846_04407, NCTC7922_05075, NCTC7927_05177, NCTC7928_03743, NCTC8009_08326, NCTC8179_05022, NCTC8621_04799, NCTC8959_04132, NCTC8960_02264, NCTC8985_03936, NCTC9001_04561, NCTC9007_01043, NCTC9036_04577, NCTC9044_02378, NCTC9045_05471, NCTC9050_02746, NCTC9055_01590, NCTC9058_02211, NCTC9062_03515, NCTC9073_00755, NCTC9077_05829, NCTC9081_06397, NCTC9111_04889, NCTC9117_05822, NCTC9119_04984, NCTC9434_04602, NCTC9701_04926, NCTC9702_05565, NCTC9703_04146, NCTC9706_01937, NCTC9777_01051, NCTC9962_03719, NCTC9969_04855, PGD_03216, PU06_05790, RG28_25645, RK56_017085, RX35_03825, SAMEA3472043_01946, SAMEA3472044_04487, SAMEA3472047_04009, SAMEA3472055_01604, SAMEA3472056_04390, SAMEA3472070_04043, SAMEA3472080_00231, SAMEA3472090_02852, SAMEA3472108_01696, SAMEA3472110_00875, SAMEA3472112_01208, SAMEA3472114_02039, SAMEA3472147_04803, SAMEA3484427_03830, SAMEA3484429_02475, SAMEA3484434_03756, SAMEA3485101_02956, SAMEA3752372_01305, SAMEA3752553_02498, SAMEA3752557_02189, SAMEA3752559_00285, SAMEA3752620_03709, SAMEA3753064_01449, SAMEA3753097_04412, SAMEA3753164_04167, SAMEA3753290_01938, SAMEA3753300_00786, SK85_04379, SY51_23235, U12A_04345, U14A_04341, UC41_10590, UN86_02805, UN91_08555, WQ89_14700, WR15_07670, YDC107_2768 Production host: ![]() ![]() #2: Antibody | Mass: 14598.097 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: C-terminus tag is not visible in the electron density maps Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M calcium chloride, 0.1 M HEPES, 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.02 Å / Num. obs: 38956 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3820 / CC1/2: 0.72 / % possible all: 99.92 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1jhc Resolution: 2.8→47.97 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 200.17 Å2 / Biso mean: 86.94 Å2 / Biso min: 43.03 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→47.97 Å
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