LYSINE-SPECIFICDEMETHYLASE2A / CXXC-TYPE ZINC FINGER PROTEIN 8 / F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11 / F-BOX PROTEIN FBL7 / F- ...CXXC-TYPE ZINC FINGER PROTEIN 8 / F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11 / F-BOX PROTEIN FBL7 / F-BOX PROTEIN LILINA / F-BOX/LRR-REPEAT PROTEIN 11 / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A / [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A
Mass: 13319.508 Da / Num. of mol.: 2 / Fragment: CXXC AND PHD DOMAIN, RESIDUES 567-681 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q9Y2K7, [histone H3]-dimethyl-L-lysine36 demethylase
Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.92 Å / Relative weight: 1
Reflection
Resolution: 2.24→90.79 Å / Num. obs: 13091 / % possible obs: 98.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 39.61 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16
Reflection shell
Resolution: 2.24→2.36 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.8 / % possible all: 98.2
-
Processing
Software
Name
Version
Classification
BUSTER
2.11.2
refinement
autoPROC
datareduction
AP_SCALE
datascaling
SHARP
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.24→90.79 Å / Cor.coef. Fo:Fc: 0.9194 / Cor.coef. Fo:Fc free: 0.8894 / SU R Cruickshank DPI: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.176 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2209
643
4.93 %
RANDOM
Rwork
0.1969
-
-
-
obs
0.1981
13045
98.98 %
-
Displacement parameters
Biso mean: 48.63 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-11.9938 Å2
0 Å2
6.3255 Å2
2-
-
8.5589 Å2
0 Å2
3-
-
-
3.4349 Å2
Refine analyze
Luzzati coordinate error obs: 0.311 Å
Refinement step
Cycle: LAST / Resolution: 2.24→90.79 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1564
0
12
106
1682
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
1592
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.09
2139
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
750
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
32
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
238
HARMONIC
5
X-RAY DIFFRACTION
t_it
1592
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
2
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.41
X-RAY DIFFRACTION
t_other_torsion
2.95
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
204
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
1756
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.24→2.42 Å / Total num. of bins used: 7
Rfactor
Num. reflection
% reflection
Rfree
0.2343
136
5.1 %
Rwork
0.1996
2530
-
all
0.2015
2666
-
obs
-
-
98.98 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.3334
-0.6868
1.1002
2.0309
-2.9205
3.6596
0.0444
-0.0131
0.0308
0.205
-0.0626
-0.0736
-0.3318
0.2827
0.0181
0.0153
0.0121
-0.0536
-0.0778
-0.0313
-0.0405
4.191
17.106
65.8942
2
1.4599
1.5757
-2.1276
2.5425
-2.8803
4.3012
0.0013
0.3406
0.0871
-0.1763
0.1028
-0.1209
0.1941
-0.0664
-0.1041
-0.0532
0.0064
0.0381
-0.0139
0.0218
-0.0864
-21.5774
-15.47
71.4614
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
+
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