1W74 | pdb_00001w74

X-ray structure of peptidyl-prolyl cis-trans isomerase A, PpiA, Rv0009, from Mycobacterium tuberculosis.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AWR	PDB ENTRY 1AWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		PROTEIN WAS CO-CRYSTALLIZED WITH THE PEPTIDE HAGPIA (FINAL CONCENTRATION 1 MM) FROM 30% PEG-200, 5% PEG-3000, 0.1 M MES-HCL PH 6.0; THEN SOAKED IN THE RESERVOIR SOLUTION PLUS 1 MM HAGPIA.

Crystal Properties
Matthews coefficient	Solvent content
3.1	60

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.349	α = 90
b = 65.349	β = 90
c = 102.493	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC CCD	SAGITALLY FOCUSING GE(220) AND A MULTILAYER	2004-02-01	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	32.62	99.6	0.1	6.2	5.4		14896

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	99.8		0.59	1.3	5.4

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 ENTRY 1AWR	2.6	30	14230	756	99.7	0.213	0.212	0.22	0.229	0.24	RANDOM	61.82

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]
5.21	2.6		5.21		-7.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.826
r_scangle_it	3.268
r_scbond_it	1.779
r_angle_refined_deg	1.404
r_mcangle_it	1.377
r_angle_other_deg	1.011
r_mcbond_it	0.71
r_symmetry_vdw_other	0.395
r_symmetry_vdw_refined	0.265
r_nbd_other	0.25
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.185
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2562
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing