3RFY | pdb_00003rfy

Crystal structure of arabidopsis thaliana cyclophilin 38 (ATCYP38)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	293	20% PEG 6000, 2.5% T-BUTANOL, 100MM SODIUM CITRATE (PH 5.5), VAPOR BATCH, TEMPERATURE 293K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.93	57.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.69	α = 90
b = 96.72	β = 90
c = 166.82	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	CCD	ADSC QUANTUM 210	VERTICALLY COLLIMATING MIRROR	2006-06-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9797, 0.9794, 0.9500	NSLS	X12C

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	2.39	50	98.6	0.067	19.21	6.4		19441		1	43.4

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	2.45	2.55	91.6		0.23	5.1	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.39	19.89	16411	669	86.9	0.248	0.248	0.26	0.266	0.29	RANDOM	69.1

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]
6.49			-3.78		-2.71

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.2
c_scangle_it	5.24
c_scbond_it	4.05
c_mcangle_it	3.68
c_angle_deg	2.9
c_improper_angle_d	2.17
c_mcbond_it	2.16
c_bond_d	0.016
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2765
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SnB	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling