3PZY | pdb_00003pzy

Crystal structure of Molybdopterin biosynthesis mog protein from Mycobacterium paratuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OI9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	290	Internal tracking number 217822A1. PACT screen condition A1: SPG buffer, pH 4, 25% PEG1500, with protein (MypaA.00778.b.A1 PW29403) at 24.39 mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.65	α = 90
b = 68.65	β = 90
c = 52.83	γ = 120

Symmetry
Space Group	P 63

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 315		2010-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976504	ALS	5.0.3

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	1.8	19.75	99.3	0.042	24.39	5.48889	13236	13146		-3	33.133

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	1.8	1.85	99.6		0.519	3.3	5.544979	960

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 (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	FOURIER SYNTHESIS	THROUGHOUT	3OI9	1.8	19.75	13236	13128	646	99.18	0.195	0.195	0.193	0.21	0.228	0.24	RANDOM	26.401

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]
0.7	0.35		0.7		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_3_deg	13.59
r_dihedral_angle_4_deg	12.212
r_dihedral_angle_1_deg	5.258
r_scangle_it	4.029
r_scbond_it	2.425
r_angle_refined_deg	1.566
r_mcangle_it	1.507
r_angle_other_deg	0.989
r_mcbond_it	0.922

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_3_deg	13.59
r_dihedral_angle_4_deg	12.212
r_dihedral_angle_1_deg	5.258
r_scangle_it	4.029
r_scbond_it	2.425
r_angle_refined_deg	1.566
r_mcangle_it	1.507
r_angle_other_deg	0.989
r_mcbond_it	0.922
r_mcbond_other	0.274
r_chiral_restr	0.092
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1024
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.