3RCF | pdb_00003rcf

Human cyclophilin D complexed with N-[(4-aminophenyl)sulfonyl]benzamide

X-RAY DIFFRACTION

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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
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.518	α = 90
b = 57.518	β = 90
c = 87.564	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	CCD	ADSC QUANTUM 4		2007-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.15	27.3	98.2	0.065		7.3	50252	49247	19.9	19.9

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	1.15	1.18	90.9		0.263		6.3

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 2BIT	1.15	26.03	50252	49247	2583	98.06	0.126	0.1264	0.12516	0.14	0.15	0.16	RANDOM	5.305

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]
0.01			0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.275
r_dihedral_angle_4_deg	15.075
r_dihedral_angle_3_deg	10.334
r_dihedral_angle_1_deg	5.958
r_sphericity_free	1.979
r_scangle_it	1.295
r_angle_refined_deg	1.164
r_sphericity_bonded	1.097
r_scbond_it	1.033
r_mcangle_it	0.856
r_angle_other_deg	0.826
r_mcbond_it	0.588
r_rigid_bond_restr	0.456
r_nbd_refined	0.223
r_mcbond_other	0.202
r_nbd_other	0.189
r_symmetry_vdw_other	0.189
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.127
r_nbtor_other	0.085
r_symmetry_hbond_refined	0.079
r_chiral_restr	0.075
r_symmetry_vdw_refined	0.074
r_bond_refined_d	0.006
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1237
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	38

Software

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