3MW7 | pdb_00003mw7

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.4	293	Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.29	α = 90
b = 61.742	β = 111.64
c = 71.212	γ = 90

Symmetry
Space Group	P 1 21 1

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		2007-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 1-BM-C	0.90020	APS	1-BM-C

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	2.3	50	83.5	0.106	0.106	10.2	3.3	20675	19597

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	2.3	2.34	49.8		0.33	0.33	1.84	1.8	626

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	2P1F	2.32	50	19597	1065	82.97	0.20758	0.20452	0.2	0.26532	0.26	RANDOM	35.443

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]
4.01		6.55	-3.19		4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.446
r_dihedral_angle_4_deg	18.136
r_dihedral_angle_3_deg	17.808
r_dihedral_angle_1_deg	6.817
r_scangle_it	3.533
r_scbond_it	2.191
r_angle_refined_deg	1.606
r_mcangle_it	1.46
r_mcbond_it	0.898
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.446
r_dihedral_angle_4_deg	18.136
r_dihedral_angle_3_deg	17.808
r_dihedral_angle_1_deg	6.817
r_scangle_it	3.533
r_scbond_it	2.191
r_angle_refined_deg	1.606
r_mcangle_it	1.46
r_mcbond_it	0.898
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.23
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3937
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	44

Software

Software
Software Name	Purpose
HKL-2000	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 R01GM157729.