6DQQ | pdb_00006dqq

Crystal structure of Haemophilus influenzae OppA complex with endogenous peptide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.1M sodium acetate pH 4.6 and 2.4M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.99	α = 90
b = 90.898	β = 90
c = 108.778	γ = 90

Symmetry
Space Group	P 21 21 21

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		2017-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0782	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.85	46.67	99.4	0.079	0.082	0.022	0.999	18.6	13.3		42868

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	1.85	1.89	99.5		0.556	0.577	0.154	0.972		13.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	46.67	40635	2168	99.29	0.1553	0.1529	0.17	0.2019	0.22	RANDOM	32.37

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]
5.04			-1.8		-3.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.22
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_4_deg	11.605
r_dihedral_angle_1_deg	6.404
r_angle_refined_deg	1.398
r_angle_other_deg	0.954
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.22
r_dihedral_angle_3_deg	13.385
r_dihedral_angle_4_deg	11.605
r_dihedral_angle_1_deg	6.404
r_angle_refined_deg	1.398
r_angle_other_deg	0.954
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4177
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
ARP/wARP	model building

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.