2R99

Crystal structure of cyclophilin ABH-like domain of human peptidylprolyl isomerase E isoform 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BIT	PDB entry 2BIT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	34% PEG 8000, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.635	α = 90
b = 66.635	β = 90
c = 77.351	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS HTC	MIRRORS	2005-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.61	40	97.3	0.041	34.34			22683		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.61	1.67	81.4		0.16	6.36	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 2BIT	1.61	33.4	21499	1157	97.4	0.164	0.162	0.17	0.196	0.2	RANDOM	25.17

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]
-0.34			-0.34		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.448
r_dihedral_angle_3_deg	11.079
r_dihedral_angle_4_deg	8.991
r_dihedral_angle_1_deg	5.795
r_rigid_bond_restr	3.934
r_scangle_it	3.86
r_scbond_it	3.72
r_sphericity_free	3.529
r_sphericity_bonded	2.728
r_mcangle_it	1.599
r_angle_refined_deg	1.197
r_mcbond_it	1.12
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.188
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1265
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling