Experiment: 5H2U

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M tri-Lithium citrate, 20 %(w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.881	α = 81.36
b = 77.018	β = 75.76
c = 87.413	γ = 74.92

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	VariMax HR	2015-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54789

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	2.24	84.52	94.7	0.099	9.3	2.4		58073

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.24	2.32	83.1		0.487	1.5	1.9

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	5D7V	2.24	84.52	52220	2789	94.46	0.2083	0.2055	0.2601	RANDOM	33.687

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]
0.85	-0.52	0.96	0.23	-0.05	-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.871
r_dihedral_angle_3_deg	17.93
r_dihedral_angle_4_deg	15.896
r_dihedral_angle_1_deg	5.844
r_scangle_it	1.913
r_angle_refined_deg	1.31
r_scbond_it	1.212
r_mcangle_it	0.834
r_mcbond_it	0.49
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.871
r_dihedral_angle_3_deg	17.93
r_dihedral_angle_4_deg	15.896
r_dihedral_angle_1_deg	5.844
r_scangle_it	1.913
r_angle_refined_deg	1.31
r_scbond_it	1.212
r_mcangle_it	0.834
r_mcbond_it	0.49
r_nbtor_refined	0.299
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.204
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8541
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	236

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.