3DA8 | pdb_00003da8

Crystal structure of PurN 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	1MEO	PDB entry 1MEO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% PEG 3350, 0.1 M Mg formate, 0.1 M NaI, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.273	α = 90
b = 73.366	β = 90
c = 77.246	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD		2007-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97900	SSRL	BL9-2

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	1.25	52.225	100	0.066	24.2	14.4		115083

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)
	1.25	1.32	100		0.822	3.6	14.1

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 (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 1MEO	1.3	36.69	112329	102250	5129	99.53	0.16487	0.16374	0.2	0.18602	0.21	RANDOM	12.078

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]
0.16			-0.1		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.496
r_dihedral_angle_4_deg	14.491
r_dihedral_angle_3_deg	10.863
r_dihedral_angle_1_deg	5.584
r_sphericity_free	4.353
r_sphericity_bonded	4.135
r_scangle_it	3.625
r_scbond_it	2.409
r_mcangle_it	1.843
r_angle_refined_deg	1.335
r_rigid_bond_restr	1.17
r_mcbond_it	1.115
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement