2Z6W

Crystal structure of human cyclophilin D in complex with cyclosporin A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		2.9		20% PEG 3350, PH 2.9, VAPOR DIFFUSION, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.882	α = 90
b = 69.313	β = 90
c = 112.077	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU		SPring-8	BL41XU

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	0.96	200	97.7	0.059	18.6	2.8		180558		-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	0.96	0.97	96.6		0.414	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2BIT	0.96	56.08	171367	9131	97.6	0.13	0.129	0.153	RANDOM	8.23

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]
0.4			-0.47		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.258
r_dihedral_angle_4_deg	16.427
r_dihedral_angle_3_deg	12.557
r_sphericity_free	9.446
r_dihedral_angle_1_deg	6.576
r_sphericity_bonded	5.116
r_scangle_it	3.776
r_scbond_it	2.853
r_mcangle_it	2.339
r_angle_refined_deg	1.826
r_mcbond_it	1.732
r_rigid_bond_restr	1.54
r_nbtor_refined	0.323
r_nbd_refined	0.251
r_symmetry_vdw_refined	0.233
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
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	2650
Nucleic Acid Atoms
Solvent Atoms	524
Heterogen Atoms	13

Software

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