3R57 | pdb_00003r57

Human Cyclophilin D Complexed with a Fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	291	30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.43	α = 90
b = 57.43	β = 90
c = 87.975	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	100	AREA DETECTOR	MARRESEARCH		2008-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	22.2	98.4	0.043		8	16586	15710	21.1	34.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.75	90.5		0.082

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.71	22	16586	15710	823	99.28	0.14036	0.13829	0.1372	0.18094	0.1792	RANDOM	9.333

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]
0.07			0.07		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.458
r_dihedral_angle_4_deg	12.005
r_dihedral_angle_3_deg	10.989
r_dihedral_angle_1_deg	5.782
r_scangle_it	1.19
r_sphericity_free	1.143
r_angle_refined_deg	1.022
r_scbond_it	0.738
r_sphericity_bonded	0.633
r_mcangle_it	0.519
r_rigid_bond_restr	0.435
r_mcbond_it	0.306
r_chiral_restr	0.074
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1240
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	57

Software

Software
Software Name	Purpose
MAR345dtb	data collection
X-PLOR	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing