3RDC | pdb_00003rdc

Human Cyclophilin D Complexed with an Inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BIT	PDB ENTRY 2BIT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	291	30% PEG4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.445	α = 90
b = 56.445	β = 90
c = 86.995	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	AREA DETECTOR	MARRESEARCH		2008-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU

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	1.93	28.2	97.5	0.059		4.1	10623	10358		9.1

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	1.93	1.987	84		0.188	3.5	4.8

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 (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 2BIT	1.94	25.79	10623	10358	529	98.99	0.20781	0.20461	0.2076	0.27014	0.2746	RANDOM	12.287

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]
-0.58			-0.58		1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.292
r_dihedral_angle_4_deg	12.106
r_dihedral_angle_3_deg	10.362
r_dihedral_angle_1_deg	5.879
r_scangle_it	1.477
r_angle_refined_deg	1.063
r_scbond_it	0.97
r_angle_other_deg	0.809
r_mcangle_it	0.605
r_mcbond_it	0.349
r_mcbond_other	0.084
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1232
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	18

Software

Software
Software Name	Purpose
MAR345dtb	data collection
X-PLOR	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing