7Q5C | pdb_00007q5c

Crystal structure of OmpG in space group 96

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	294	30-60 mM Sodium Citrate, 50-70mM NaCl, 12-14 % (w/v) PEG-3350, 60-65 mM n-octyl-beta-d-glucoside, 6-12 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
4.41	72.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.343	α = 90
b = 71.343	β = 90
c = 200.464	γ = 90

Symmetry
Space Group	P 43 21 2

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 9M		2019-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.97918	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.717	67.304	99.7	0.0247	16.9	2		14670

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.717	2.788			0.83

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2iwv	2.717	67.304	14670	1453	99.633	0.278	0.274	0.27	0.328	0.33	77.184

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]
-3.734			-3.734		7.469

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.74
r_dihedral_angle_4_deg	25.072
r_dihedral_angle_3_deg	19.056
r_lrange_it	14.11
r_lrange_other	14.107
r_scangle_it	11.435
r_scangle_other	11.433
r_mcangle_it	10.614
r_mcangle_other	10.612
r_dihedral_angle_1_deg	9.862
r_scbond_it	8.159
r_scbond_other	8.156
r_mcbond_it	7.503
r_mcbond_other	7.499
r_angle_other_deg	2.503
r_angle_refined_deg	1.858
r_symmetry_nbd_other	0.23
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.197
r_nbtor_refined	0.189
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.075
r_bond_other_d	0.036
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2056
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
xia2	data reduction
XDS	data scaling
MOLREP	phasing