1M9C | pdb_00001m9c

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type 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 ENTRY 1AK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294	PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.09	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.445	α = 90
b = 113.235	β = 100.53
c = 67.006	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		1997-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.0	NSLS	X12C

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	2	38	83	0.063	0.063	14.8	2.8	38057	31588	-3	-3	35.4

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)
	2	2.03	60		0.195	0.195	2.8	1.55	1153

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1AK4	2	37.8	-3	28437	3125	82.95	0.20128	0.201	0.19506	0.2	0.25934	0.26	RANDOM	29.841

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]
-1.95		-0.4	3.71		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.12
r_dihedral_angle_1_deg	5.066
r_scangle_it	3.86
r_mcangle_it	3.824
r_scbond_it	2.723
r_angle_refined_deg	2.704
r_mcbond_it	2.687
r_angle_other_deg	1.634
r_symmetry_hbond_refined	0.256
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.184
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.162
r_nbd_other	0.162
r_symmetry_vdw_other	0.162
r_symmetry_hbond_other	0.141
r_nbtor_other	0.031
r_xyhbond_nbd_other	0.027
r_bond_refined_d	0.018
r_gen_planes_refined	0.015
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4712
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

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