4J07

Crystal structure of a PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-dimethyl-8-ribityllumazine synthase, DMRL synthase, Lumazine synthase) from Mycobacterium leprae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	MD Morpheus screen C12: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 30mM sodium-nitrate, 30mM di-sodium hydrogen phosphate, 30mM ammonium sulfate, 100mM Bicine/Trizma base pH 8.5; MyleA.00730.a.A1.PS00659 at 20mg/ml; direct cryo, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.71	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.95	α = 90
b = 109.95	β = 90
c = 288.33	γ = 120

Symmetry
Space Group	P 65 2 2

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	RIGAKU SATURN 944+		2011-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.95	50	99.6	0.121	19.05	17.9	76305	75991		-3	27.672

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	1.95	2	96.4		0.523	4.16	8.15

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1W19	1.95	45.25	76305	71727	3829	99.6	0.2101	0.2101	0.2081	0.2461	RANDOM	22.737

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]
-0.05	-0.05		-0.05		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.971
r_dihedral_angle_4_deg	14.554
r_dihedral_angle_3_deg	13.141
r_dihedral_angle_1_deg	5.597
r_angle_refined_deg	1.521
r_mcangle_it	1.502
r_mcbond_it	0.939
r_mcbond_other	0.938
r_angle_other_deg	0.778
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.971
r_dihedral_angle_4_deg	14.554
r_dihedral_angle_3_deg	13.141
r_dihedral_angle_1_deg	5.597
r_angle_refined_deg	1.521
r_mcangle_it	1.502
r_mcbond_it	0.939
r_mcbond_other	0.938
r_angle_other_deg	0.778
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5354
Nucleic Acid Atoms
Solvent Atoms	467
Heterogen Atoms	35

Software

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

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 R01GM133198.