Experiment: 1VK5

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	protein (10 mg/ml), Ammonium Sulfate (0.8M), Hepes (0.1M), Magnesium Sulfate (0.04M), CHAPS (0.41%), pH 8.5, Vapor diffusion, hanging drop, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	8.5	293	protein (5 mg/ml), Ammonium Sulfate (0.8M), Hepes (0.1M), Magnesium Sulfate (0.04M), CHAPS (0.41%), pH 8.5, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.45	α = 90
b = 83.45	β = 90
c = 60.575	γ = 120

Symmetry
Space Group	P 31 2 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	CCD	ADSC QUANTUM 4	Bent cylindrical Si-mirror (Rh coating)	2004-02-14	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MAR CCD 165 mm	Rh Mirror	2004-02-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9790	APS	14-BM-D
2	SYNCHROTRON	APS BEAMLINE 32-ID	0.96408, 0.97916, 0.97931	APS	32-ID

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	1.6	50	99.2	0.037	38.61	10.9		32231

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	1.6	1.66	92.2		0.302	9.3	10.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.604	34.3	30570	1633	99.99	0.161	0.16102	0.1599	0.1835	RANDOM	23.618

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.359
r_dihedral_angle_1_deg	4.689
r_scbond_it	3.626
r_mcangle_it	2.821
r_angle_refined_deg	1.646
r_mcbond_it	1.495
r_nbtor_refined	0.321
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.202

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	5.359
r_dihedral_angle_1_deg	4.689
r_scbond_it	3.626
r_mcangle_it	2.821
r_angle_refined_deg	1.646
r_mcbond_it	1.495
r_nbtor_refined	0.321
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.212
r_xyhbond_nbd_refined	0.202
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1003
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	63

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

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.