3BK0

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Complexed with 5-CN-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
2.31	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.552	α = 90
b = 61.554	β = 111.81
c = 70.989	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	MARMOSAIC 225 mm CCD	DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror	2007-08-15	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	1.6	50	78.5	0.058	0.058	14.6	3.3	58529	58523

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	1.6	1.66	21.7		0.323	0.323	1.95	1.7	1607

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2P1F	1.6	50	58529	55585	2938	78.25	0.18102	0.17919	0.21562	RANDOM	22.348

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]
0.6		1.85	-1.27		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.328
r_dihedral_angle_4_deg	16.749
r_dihedral_angle_3_deg	12.79
r_dihedral_angle_1_deg	6.039
r_scangle_it	3.951
r_scbond_it	2.475
r_angle_refined_deg	1.514
r_mcangle_it	1.486
r_mcbond_it	0.969
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.328
r_dihedral_angle_4_deg	16.749
r_dihedral_angle_3_deg	12.79
r_dihedral_angle_1_deg	6.039
r_scangle_it	3.951
r_scbond_it	2.475
r_angle_refined_deg	1.514
r_mcangle_it	1.486
r_mcbond_it	0.969
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.1
r_bond_refined_d	0.01
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3934
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
MxDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

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.