Experiment: 5VZP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-HCl, 1 mM EDTA, pH 9 2.5 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.132	α = 90
b = 90.132	β = 90
c = 45.248	γ = 120

Symmetry
Space Group	P 6

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		2013-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	99.3	0.054	0.058	0.021	32.6	7		20200

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	1.78	1.81	86.9		0.084	0.096	0.044	0.989		4.3

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	2MBW	1.78	31.95	19105	1026	99.52	0.1546	0.1525	0.1928	RANDOM	18.933

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]
0.04	0.04		0.04		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.58
r_dihedral_angle_4_deg	23.217
r_dihedral_angle_3_deg	13.924
r_dihedral_angle_1_deg	5.185
r_angle_refined_deg	2.443
r_mcangle_it	2.336
r_mcbond_it	1.906
r_mcbond_other	1.782
r_angle_other_deg	0.995
r_chiral_restr	0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.58
r_dihedral_angle_4_deg	23.217
r_dihedral_angle_3_deg	13.924
r_dihedral_angle_1_deg	5.185
r_angle_refined_deg	2.443
r_mcangle_it	2.336
r_mcbond_it	1.906
r_mcbond_other	1.782
r_angle_other_deg	0.995
r_chiral_restr	0.15
r_bond_refined_d	0.023
r_gen_planes_refined	0.013
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1216
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	99

Software

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

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.