Experiment: 6UMJ

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	0.1 M sodium acetate, pH 5.0, 30% MPD, 5% 1,3-butanediol

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.481	α = 90
b = 73.481	β = 90
c = 177.167	γ = 120

Symmetry
Space Group	P 32 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	RIGAKU SATURN 944	VariMax HF	2014-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	2.7	30	98.9	0.171	0.176	0.038	7.1	21.5		15692

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	2.7	2.8	98		0.744	0.761	0.161	0.95		21.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.7	30	14829	803	98.64	0.2269	0.2248	0.2671	RANDOM	58.851

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]
0.18	0.09		0.18		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.052
r_dihedral_angle_4_deg	13.945
r_dihedral_angle_3_deg	13.272
r_dihedral_angle_1_deg	4.744
r_angle_refined_deg	0.836
r_angle_other_deg	0.64
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.052
r_dihedral_angle_4_deg	13.945
r_dihedral_angle_3_deg	13.272
r_dihedral_angle_1_deg	4.744
r_angle_refined_deg	0.836
r_angle_other_deg	0.64
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3358
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	22

Software

Software
Software Name	Purpose
StructureStudio	data collection
DENZO	data reduction
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
PHASER	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
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 R01GM133198.