3ICH | pdb_00003ich

Crystal structure of cyclophilin B at 1.2 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CYN	PDB entry 1CYN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	25% w/v PEG 1500, 0.1M MMT buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.665	α = 90
b = 64.665	β = 90
c = 39.463	γ = 120

Symmetry
Space Group	P 32

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 210	mirrors	2009-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.9795	CHESS	F2

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	1.2	50	100	0.035	49.8	5.3		54635		1

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	1.22	99.7		0.105	8.8	3.1	3989

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1CYN	1.2	50	54608	54608	2916	99.92	0.14407	0.14407	0.14312	0.14	0.16185	0.16	RANDOM	10.764

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]
-0.14	-0.07		-0.14		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.763
r_dihedral_angle_4_deg	20.182
r_dihedral_angle_3_deg	9.366
r_dihedral_angle_1_deg	5.921
r_scangle_it	2.163
r_sphericity_free	1.885
r_scbond_it	1.585
r_sphericity_bonded	1.522
r_rigid_bond_restr	1.239
r_angle_refined_deg	1.118
r_mcangle_it	0.977
r_mcbond_it	0.623
r_nbtor_refined	0.313
r_nbd_refined	0.178
r_symmetry_vdw_refined	0.146
r_chiral_restr	0.076
r_xyhbond_nbd_refined	0.076
r_symmetry_hbond_refined	0.071
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1399
Nucleic Acid Atoms
Solvent Atoms	376
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling