5A0E | pdb_00005a0e

Crystal structure of cyclophilin D in complex with CsA analogue, JW47.

X-RAY DIFFRACTION

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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, HANGING DROP	2.9		HANGING DROP 50:50. PRECIPITANT: 23% POLYETHYLENE GLYCOL (PEG3350), 50 MM SODIUM-CITRATE BUFFER AT PH 2.9 PROTEIN: 30 MG/ML IN 50MM POTASSIUM/SODIUM PHOSPHATE PH 7.3, 100MM NACL, 2MM EDTA, 0.02% SODIUM AZIDE.

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.12	α = 90
b = 69.51	β = 90
c = 109.17	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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2015-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	1.12	35.99	90.5	0.06	20.4	11.8		101898

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	1.12	1.15	45.8		1.04	1.8	6.7

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 2Z6W	1.25	35.99	75156	3964	97.48	0.09971	0.09806	0.12	0.13122	0.14	RANDOM	15.02

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]
-0.01					0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	30.806
r_dihedral_angle_2_deg	28.953
r_dihedral_angle_4_deg	17.751
r_dihedral_angle_3_deg	11.976
r_sphericity_bonded	11.736
r_dihedral_angle_1_deg	6.765
r_rigid_bond_restr	6.193
r_scbond_it	4.204
r_mcangle_it	3.3
r_angle_other_deg	3.101
r_mcbond_it	2.678
r_mcbond_other	2.677
r_angle_refined_deg	2.137
r_chiral_restr	0.3
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2680
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing