Experiment: 5GZ1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WYB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.364	α = 90
b = 83.201	β = 90
c = 142.241	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r	silicon single crystal	2014-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.78	50	98.2	0.043	31.7	7.1		65090

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	99.5		0.303	0.966		7.2

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	3wyb	1.78	50	61822	3209	98.18	0.1831	0.1806	0.2314	RANDOM	33.494

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]
0.7			-0.36		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.952
r_dihedral_angle_4_deg	18.029
r_dihedral_angle_3_deg	14.696
r_dihedral_angle_1_deg	6.455
r_mcangle_it	4.315
r_mcbond_it	3.274
r_mcbond_other	3.269
r_angle_refined_deg	2.033
r_angle_other_deg	0.952
r_chiral_restr	0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.952
r_dihedral_angle_4_deg	18.029
r_dihedral_angle_3_deg	14.696
r_dihedral_angle_1_deg	6.455
r_mcangle_it	4.315
r_mcbond_it	3.274
r_mcbond_other	3.269
r_angle_refined_deg	2.033
r_angle_other_deg	0.952
r_chiral_restr	0.142
r_bond_refined_d	0.023
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5004
Nucleic Acid Atoms
Solvent Atoms	441
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data reduction

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.