3QYU | pdb_00003qyu

Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6W	PDB entry 2Z6W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	291	30% Peg 4000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.927	α = 90
b = 57.927	β = 90
c = 88.537	γ = 90

Symmetry
Space Group	P 41 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	298	CCD	ADSC QUANTUM 315r		2010-07-25	M	SINGLE WAVELENGTH
2	1	x-ray	298	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.97964	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2	1.54	28.976	86.2		3.6	19640	18518

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)
1,2	1.54	1.62	82.1		0.299	2.2	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	isomorphous	THROUGHOUT	PDB entry 2Z6W	1.54	27.53	2	19640	18518	982	86.2	0.151	0.14974	0.1476	0.16	0.1894	0.2	RANDOM	13.386

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			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.86
r_dihedral_angle_4_deg	15.77
r_dihedral_angle_3_deg	12.807
r_dihedral_angle_1_deg	5.79
r_scangle_it	3.209
r_scbond_it	2.185
r_mcangle_it	1.501
r_angle_refined_deg	1.23
r_mcbond_it	0.921
r_angle_other_deg	0.883

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.86
r_dihedral_angle_4_deg	15.77
r_dihedral_angle_3_deg	12.807
r_dihedral_angle_1_deg	5.79
r_scangle_it	3.209
r_scbond_it	2.185
r_mcangle_it	1.501
r_angle_refined_deg	1.23
r_mcbond_it	0.921
r_angle_other_deg	0.883
r_rigid_bond_restr	0.837
r_mcbond_other	0.245
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1230
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

Software
Software Name	Purpose
DNA	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.