Experiment: 7KBY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QCB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	295	26 mg/mL 2.0 M ammonium sulfate, 0.1 M sodium acetate pH 4

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.56	α = 90
b = 57.56	β = 90
c = 183.45	γ = 90

Symmetry
Space Group	I 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2019-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	45.86	100	0.21	0.22	0.063	0.997	9.1	11.7		17537

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	100		1.84	1.922	0.549	0.38		11.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QCB	1.7	41.95	16550	956	99.92	0.1936	0.1919	0.2241	RANDOM	20.95

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.56			-0.56		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.941
r_dihedral_angle_4_deg	19.118
r_dihedral_angle_3_deg	13.985
r_dihedral_angle_1_deg	8.152
r_angle_other_deg	2.96
r_angle_refined_deg	2.685
r_chiral_restr	0.072
r_bond_other_d	0.038
r_gen_planes_other	0.018
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.941
r_dihedral_angle_4_deg	19.118
r_dihedral_angle_3_deg	13.985
r_dihedral_angle_1_deg	8.152
r_angle_other_deg	2.96
r_angle_refined_deg	2.685
r_chiral_restr	0.072
r_bond_other_d	0.038
r_gen_planes_other	0.018
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	928
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	42

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.