5NOW | pdb_00005now

Structure of cyclophilin A in complex with pyridine-3,4-diamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LUD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	279.15	PEG 8000, Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.77	α = 90
b = 54.67	β = 90
c = 86.97	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 2M		2014-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.920	Diamond	I04-1

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	1.48	23.14	89.8	0.08	12.8	6		31129

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	1.48	1.52	66.8		0.56	2.2	4.3	1685

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	5LUD	1.48	23.03	29517	1568	89.46	0.20258	0.20166	0.21	0.21949	0.23	RANDOM	17.979

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]
0.35			-0.46		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.75
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_4_deg	12.332
r_dihedral_angle_1_deg	6.392
r_long_range_B_refined	5.022
r_long_range_B_other	5.02
r_scangle_other	3.421
r_mcangle_it	2.392
r_mcangle_other	2.391
r_scbond_it	2.291
r_scbond_other	2.29
r_angle_refined_deg	2.066
r_mcbond_it	1.631
r_mcbond_other	1.63
r_angle_other_deg	1.138
r_chiral_restr	0.15
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1266
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing