3SGU | pdb_00003sgu

Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase covalently modified by 5-fluoro-6-iodo-UMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DV7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293	Trisodium Citrate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.891	α = 90
b = 103.709	β = 90
c = 73.68	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARMOSAIC 225 mm CCD		2008-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-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	1.7	50	94.9	0.059	14	5.7	23657	22900

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	1.7	1.76	65		0.232	2.8	1.9	1592

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	1DV7	1.7	26.94	22433	1204	94.54	0.16576	0.16416	0.16	0.19614	0.2	RANDOM	18.669

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]
0.87			-1.15		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.499
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	12.609
r_dihedral_angle_1_deg	5.494
r_scangle_it	4.3
r_scbond_it	2.487
r_mcangle_it	1.549
r_angle_refined_deg	1.467
r_mcbond_it	0.864
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.499
r_dihedral_angle_4_deg	19.853
r_dihedral_angle_3_deg	12.609
r_dihedral_angle_1_deg	5.494
r_scangle_it	4.3
r_scbond_it	2.487
r_mcangle_it	1.549
r_angle_refined_deg	1.467
r_mcbond_it	0.864
r_chiral_restr	0.103
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1617
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	22

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.