7L6Z | pdb_00007l6z

Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus pneumoniae R6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	Protein: 5.0 mg/ml, 0.01M Tris pH 8.3;Screen: PACT (B8), 0.2M Ammonium chloride, 0.1M MES pH 6.0, 20% (w/v) PEG6000.

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.432	α = 90
b = 156.529	β = 117.18
c = 90.535	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	CCD	MARMOSAIC 300 mm CCD	Be	2019-07-24	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	1.88	30	99.1	0.087	0.087	0.098	0.045	16.6	4.4		175455		-3	27.3

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	1.88	1.91	99.1		0.758	0.758	0.857	0.393	0.725	2.3	4.4

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	1.88	29.97	166357	9021	98.92	0.1748	0.1728	0.18	0.2124	0.22	RANDOM	34.069

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]
-0.64		0.9	-1.06		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.448
r_dihedral_angle_4_deg	10.811
r_dihedral_angle_3_deg	8.785
r_dihedral_angle_1_deg	3.242
r_angle_refined_deg	1.329
r_angle_other_deg	0.356
r_chiral_restr	0.064
r_gen_planes_refined	0.054
r_gen_planes_other	0.052
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.448
r_dihedral_angle_4_deg	10.811
r_dihedral_angle_3_deg	8.785
r_dihedral_angle_1_deg	3.242
r_angle_refined_deg	1.329
r_angle_other_deg	0.356
r_chiral_restr	0.064
r_gen_planes_refined	0.054
r_gen_planes_other	0.052
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16640
Nucleic Acid Atoms
Solvent Atoms	1551
Heterogen Atoms	108

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.