1M9F | pdb_00001m9f

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AK4	PDB ID 1AK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.08	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.508	α = 90
b = 110.941	β = 101.41
c = 67.932	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 4		2000-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.73	20	96	0.057	0.057	15.9	2.4	58422	56085	-3	-3	31.3

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)
	1.73	1.78	93		0.366	0.366	15.9	2.4	4548

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 ID 1AK4	1.73	19.69	-3	58422	50245	5627	96.03	0.17177	0.16654	0.18	0.21965	0.23	RANDOM	23.478

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]
-0.86		-0.1	1.45		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.405
r_dihedral_angle_1_deg	5.766
r_scangle_it	4.789
r_mcangle_it	3.804
r_scbond_it	3.146
r_angle_refined_deg	2.794
r_mcbond_it	2.598
r_angle_other_deg	1.668
r_symmetry_hbond_refined	0.244
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.217
r_symmetry_vdw_other	0.213
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.18
r_nbd_other	0.16
r_xyhbond_nbd_other	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.016
r_gen_planes_other	0.013
r_bond_other_d	0.001
r_nbtor_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4708
Nucleic Acid Atoms
Solvent Atoms	576
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	phasing