1E8K

Cyclophilin 3 Complexed With Dipeptide Ala-Pro

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DYW	PDB ENTRY 1DYW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6		MPEG5000, SODIUM CITRATE, PH 5.6

Crystal Properties
Matthews coefficient	Solvent content
3.08	59.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.035	α = 90
b = 61.035	β = 90
c = 122.66	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	COLLIMATOR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571

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	1.9	25	97.6	0.079	12.85	7.92		19230

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	1.9	1.93	88.2		0.332	2.13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ENTRY 1DYW	1.9	10	17589	934	93.4	0.1826		0.2505	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		1497.31

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.148
s_similar_adp_cmpnt	0.086
s_non_zero_chiral_vol	0.049
s_zero_chiral_vol	0.038
s_angle_d	0.028
s_from_restr_planes	0.0278
s_bond_d	0.023
s_similar_dist	0.008
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1297
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	13

Software

Software
Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.