7L71 | pdb_00007l71

Crystal Structure of the PDZ Domain of the Serine Peptidase HtrA from Streptococcus agalactiae.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	Protein: 8.0 mg/ml, 0.01M Tris pH 8.3;Screen: PACT (D4), 0.1M MMT buffer pH 7.0, 25% (w/v) PEG 1500.

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.878	α = 90
b = 29.33	β = 101.45
c = 35.827	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 300 mm CCD	Be	2019-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	0.97	30	92.8	0.082	0.082	0.088	0.032	30.9	8.2		49931		-3	8.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.97	0.99	73.9		0.787	0.787	0.846	0.304	0.904	4.7	7.4

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	SAD	THROUGHOUT	0.97	20.64	47402	2525	92.76	0.1396	0.139	0.14	0.1501	0.15	RANDOM	12.932

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]
0.04		-0.08	0.3		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.135
r_dihedral_angle_4_deg	11.319
r_dihedral_angle_3_deg	9.426
r_dihedral_angle_1_deg	5.437
r_angle_refined_deg	1.558
r_rigid_bond_restr	1.336
r_angle_other_deg	0.405
r_chiral_restr	0.073
r_gen_planes_other	0.057
r_gen_planes_refined	0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.135
r_dihedral_angle_4_deg	11.319
r_dihedral_angle_3_deg	9.426
r_dihedral_angle_1_deg	5.437
r_angle_refined_deg	1.558
r_rigid_bond_restr	1.336
r_angle_other_deg	0.405
r_chiral_restr	0.073
r_gen_planes_other	0.057
r_gen_planes_refined	0.056
r_bond_refined_d	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	811
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

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.