3MO7

Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 2'-fluoro-6-iodo-UMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P1F	PDB entry 2P1F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.499	α = 90
b = 116.035	β = 90
c = 62.103	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	DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.	2007-08-16	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)	R Sym 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	1.35	50	94.1	0.073	0.073	11.2	4.8	58884	56107

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.35	1.4	97.7		0.476	0.476	3.1	4.4	6052

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2P1F	1.35	23.61	55868	2994	94.04	0.15636	0.15533	0.17534	RANDOM	13.982

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]
1.01			-0.65		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.419
r_dihedral_angle_4_deg	13.277
r_dihedral_angle_3_deg	12.575
r_dihedral_angle_1_deg	6.129
r_scangle_it	3.558
r_scbond_it	2.21
r_angle_refined_deg	1.439
r_mcangle_it	1.327
r_mcbond_it	0.95
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.419
r_dihedral_angle_4_deg	13.277
r_dihedral_angle_3_deg	12.575
r_dihedral_angle_1_deg	6.129
r_scangle_it	3.558
r_scbond_it	2.21
r_angle_refined_deg	1.439
r_mcangle_it	1.327
r_mcbond_it	0.95
r_nbtor_refined	0.305
r_nbd_refined	0.251
r_symmetry_hbond_refined	0.222
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1974
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	27

Software

Software
Software Name	Purpose
MxDC	data collection
MOLREP	phasing
REFMAC	refinement
Coot	model building
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 R01GM133198.