Experiment: 4ZPZ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291	50 mM sodium cacodylate, 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.699	α = 90
b = 41.699	β = 90
c = 69.831	γ = 120

Symmetry
Space Group	P 31

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 6M		2015-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9797	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.538	36.113	99.7	0.067	0.08	0.044	10.2	3.1	20124	20124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.538	1.62	98.8		0.333	0.333	0.235	2.1	2.8	2910

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1UBQ	1.54	25.1	19062	1035	99.66	0.1403	0.1386	0.1533	0.1727	0.1964	RANDOM	16.231

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]
3.12			3.12		-6.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.303
r_dihedral_angle_4_deg	13.52
r_dihedral_angle_3_deg	11.631
r_dihedral_angle_1_deg	6.234
r_mcangle_it	2.943
r_mcbond_it	2.542
r_mcbond_other	2.504
r_angle_refined_deg	1.825
r_angle_other_deg	1.247
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.303
r_dihedral_angle_4_deg	13.52
r_dihedral_angle_3_deg	11.631
r_dihedral_angle_1_deg	6.234
r_mcangle_it	2.943
r_mcbond_it	2.542
r_mcbond_other	2.504
r_angle_refined_deg	1.825
r_angle_other_deg	1.247
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1166
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	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.