#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2022
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97857 Å / Relative weight: 1
Reflection
Resolution: 1.65→47 Å / Num. obs: 59530 / % possible obs: 93.9 % / Redundancy: 1.92 % / Biso Wilson estimate: 22.39 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.81
Reflection shell
Resolution: 1.65→1.67 Å / Num. unique obs: 8577 / CC1/2: 0.88 / % possible all: 84.3
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.4 (23-JAN-2024)
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→23.7 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.105 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2159
2835
4.77 %
RANDOM
Rwork
0.1881
-
-
-
obs
0.1895
59460
93.8 %
-
Displacement parameters
Biso mean: 25.4 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.6174 Å2
-0.6386 Å2
-2.9145 Å2
2-
-
-1.3215 Å2
-2.8303 Å2
3-
-
-
2.9389 Å2
Refine analyze
Luzzati coordinate error obs: 0.2 Å
Refinement step
Cycle: LAST / Resolution: 1.65→23.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4508
0
18
417
4943
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
8927
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.96
15992
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2615
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
X-RAY DIFFRACTION
t_gen_planes
1450
HARMONIC
5
X-RAY DIFFRACTION
t_it
4657
HARMONIC
10
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
4.18
X-RAY DIFFRACTION
t_other_torsion
15.29
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
568
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
8164
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.65→1.67 Å / Total num. of bins used: 51
Rfactor
Num. reflection
% reflection
Rfree
0.258
-
5.04 %
Rwork
0.2394
1130
-
all
0.2404
1190
-
obs
-
-
67.93 %
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
1.2762
-0.1104
-0.3029
0.8899
-0.144
0.789
0.2037
0.2035
0.1673
-0.0802
-0.1487
-0.0859
-0.0269
-0.0525
-0.055
-0.0065
0.0444
0.0268
-0.0045
0.0344
-0.047
-18.7415
-4.2152
-9.4314
2
1.1668
-0.3553
0.0219
0.8175
-0.0733
0.63
-0.1254
-0.1442
-0.0919
0.0939
0.1437
0.112
-0.0065
0.0266
-0.0183
-0.0275
0.0105
0.009
-0.0246
0.0083
-0.0586
-3.4815
-26.995
-40.3822
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ B|* }
2
X-RAY DIFFRACTION
2
{ A|* }
+
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