7OQK

Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 15 minutes soaking

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293.15	Ammonium sulfate, Tris/HCl, Glutathion, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.016	α = 90
b = 61.916	β = 112.95
c = 70.159	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER X 16M		2018-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.827	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.1	34.85	98.4	0.052	0.062	0.999	12.21	3.459		220012			14.315

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.13	98		0.865	1.03	0.693	1.8	3.37

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	6ZWY	1.1	34.85	209142	10880	98.54	0.1305	0.1297	0.1456	RANDOM	14.905

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]
0.03		0.49	-0.82		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.685
r_dihedral_angle_4_deg	15.431
r_dihedral_angle_3_deg	12.463
r_dihedral_angle_1_deg	6.755
r_angle_other_deg	1.521
r_angle_refined_deg	1.458
r_rigid_bond_restr	1.007
r_chiral_restr	0.081
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.685
r_dihedral_angle_4_deg	15.431
r_dihedral_angle_3_deg	12.463
r_dihedral_angle_1_deg	6.755
r_angle_other_deg	1.521
r_angle_refined_deg	1.458
r_rigid_bond_restr	1.007
r_chiral_restr	0.081
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3923
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.