4HIB | pdb_00004hib

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N4-OH

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.6M-1.7M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.78	α = 90
b = 61.64	β = 112.08
c = 71.37	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 300 mm CCD	DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing	2011-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.979490	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	1.54	50	85	0.046	13.96			70712		-3	31.727

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	1.54	1.58	32.7		0.015	0.44

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	2qcm	1.8	66.08	50390	2633	99.02	0.1952	0.19	0.19	0.223	0.22	RANDOM	29.1315

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]
1.44		1.81	-1.68		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.426
r_dihedral_angle_4_deg	19.76
r_dihedral_angle_3_deg	14.676
r_dihedral_angle_1_deg	6.443
r_scangle_it	5.262
r_scbond_it	3.667
r_angle_refined_deg	2.215
r_mcangle_it	2.177
r_mcbond_it	1.364
r_chiral_restr	0.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.426
r_dihedral_angle_4_deg	19.76
r_dihedral_angle_3_deg	14.676
r_dihedral_angle_1_deg	6.443
r_scangle_it	5.262
r_scbond_it	3.667
r_angle_refined_deg	2.215
r_mcangle_it	2.177
r_mcbond_it	1.364
r_chiral_restr	0.268
r_bond_refined_d	0.028
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3916
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	52

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Macromolecular	data collection

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.