7OQI | pdb_00007oqi

Human OMPD-domain of UMPS in complex with substrate OMP at 1.15 Angstrom resolution, 10 minutes soaking

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZWY

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	50.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.027	α = 90
b = 61.901	β = 113.01
c = 70.217	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	1.15	42.55	98.8	0.043	0.051	1	16.29	3.476		193500			15.663

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	1.15	1.18	98.8		0.784	0.931	0.638	1.82	3.449

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	6ZWY	1.15	42.55	183952	9554	98.96	0.1221	0.1213	0.1213	0.138	0.1375	RANDOM	15.162

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]
0.08		0.54	-0.72		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.651
r_dihedral_angle_4_deg	15.595
r_dihedral_angle_3_deg	12.495
r_dihedral_angle_1_deg	6.736
r_angle_other_deg	1.506
r_angle_refined_deg	1.455
r_rigid_bond_restr	0.996
r_chiral_restr	0.079
r_gen_planes_refined	0.01
r_bond_refined_d	0.007
r_gen_planes_other	0.004
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	32

Software

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