7L6Y | pdb_00007l6y

Crystal Structure of the Peptidyl-Prolyl Cis-Trans Isomerase (PpiB) from Streptococcus pyogenes.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	Protein: 8.8 mg/ml, 0.01M Tris HCl (pH 8.3);Screen: Classics II (D10), 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG5000 MME.

Crystal Properties
Matthews coefficient	Solvent content
2	37.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.251	α = 90
b = 50.532	β = 92.32
c = 106.977	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	2019-03-22	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	1.28	30	98.3	0.079	0.079	0.085	0.03	37.1	7.9		92003		-3	14.4

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	1.28	1.3	96.5		0.799	0.799	0.855	0.303	0.91	3	7.7

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	1.28	27.12	87382	4603	98.11	0.1602	0.1584	0.1581	0.1955	0.1939	RANDOM	18.803

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]
0.44		-0.01	-0.49		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.748
r_dihedral_angle_4_deg	11.734
r_dihedral_angle_3_deg	10.174
r_rigid_bond_restr	8.836
r_dihedral_angle_1_deg	4.685
r_angle_refined_deg	1.409
r_angle_other_deg	0.473
r_chiral_restr	0.067
r_gen_planes_refined	0.05
r_gen_planes_other	0.048
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3236
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms

Software

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