6VJ6

2.55 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus cereus

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 8.3 mg/ml, 0.01M Tris pH 8.3; Reservior (Screen JCSG+, G1): 0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.6	66.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.425	α = 90
b = 70.358	β = 91.749
c = 79.357	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	C(111)	2019-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.55	30	99.9	0.084	0.084	0.095	0.044	18.1	5		27237		-3	56.3

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	2.55	2.59	100		0.787	0.787	0.883	0.394	0.831	2.3	5.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.553	29.73	27229	1382	99.645	0.219	0.2174	0.2474	77.617

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]
-5.799		-1.495	-7.05		12.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.598
r_lrange_it	10.751
r_lrange_other	10.748
r_dihedral_angle_3_deg	8.763
r_dihedral_angle_4_deg	8.272
r_scangle_it	7.583
r_scangle_other	7.582
r_mcangle_it	6.322
r_mcangle_other	6.321
r_scbond_it	4.761
r_scbond_other	4.76
r_mcbond_it	4.163
r_mcbond_other	4.163
r_dihedral_angle_1_deg	1.828
r_angle_refined_deg	1.452
r_angle_other_deg	0.384
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.204
r_nbd_other	0.185
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.151
r_ncsr_local_group_1	0.123
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.07
r_gen_planes_refined	0.054
r_gen_planes_other	0.054
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4180
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	50

Software

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