Experiment: 7EKZ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	0.1 M sodium formate, 22% w/v polyethylene glycol 3550

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.1	α = 90
b = 49.59	β = 90
c = 77.094	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	PIXEL	DECTRIS PILATUS 200K		2018-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

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	1.43	23.55	98.2	0.147	0.163	0.068	0.983	5.2	4.8		33402		2

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	1.43	1.45	95.2		0.419	0.506	0.276	0.774	2	3

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	1GWY	1.43	23.55	30818	1702	95.43	0.1658	0.1628	0.2198	RANDOM	11.024

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]
-1.24			0.72		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	93.649
r_dihedral_angle_2_deg	32.331
r_dihedral_angle_4_deg	21.929
r_sphericity_bonded	20.483
r_dihedral_angle_3_deg	12.392
r_dihedral_angle_1_deg	7.28
r_rigid_bond_restr	3.871
r_angle_refined_deg	2.105
r_angle_other_deg	0.968
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	93.649
r_dihedral_angle_2_deg	32.331
r_dihedral_angle_4_deg	21.929
r_sphericity_bonded	20.483
r_dihedral_angle_3_deg	12.392
r_dihedral_angle_1_deg	7.28
r_rigid_bond_restr	3.871
r_angle_refined_deg	2.105
r_angle_other_deg	0.968
r_chiral_restr	0.117
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1283
Nucleic Acid Atoms
Solvent Atoms	345
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
BALBES	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 R01GM133198.