4DGA | pdb_00004dga

TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WLW	PDB ENTRIES 2WLW AND 1AK4
experimental model	PDB	1AK4	PDB ENTRIES 2WLW AND 1AK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	20% w/v PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.59	α = 90
b = 111.35	β = 102.39
c = 67.76	γ = 90

Symmetry
Space Group	P 1 21 1

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 315r		2010-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0720	ESRF	ID23-1

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	66.182	95.1	0.053	9.2	1.8	41766	41766			20.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	83.1		0.196	0.196	3.6	1.7	5322

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 2WLW AND 1AK4	1.9	66.18	41697	2111	94.79	0.1983	0.1959	0.2001	0.2431	0.2484	RANDOM	25.0759

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]
-0.12		-0.21	1.3		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.232
r_dihedral_angle_4_deg	18.734
r_dihedral_angle_3_deg	13.096
r_dihedral_angle_1_deg	5.785
r_angle_refined_deg	1.204
r_angle_other_deg	0.838
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4554
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PXSOFT	data collection
MOSFLM	data reduction
PHASER	phasing