2QCF | pdb_00002qcf

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain (Asp312Asn mutant) of human UMP synthase bound to 5-fluoro-UMP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.815	α = 90
b = 115.512	β = 90
c = 61.37	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	MAR CCD 165 mm		2006-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.22	22.14	99.8	0.083	21.4	6.4		81404

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.22	1.24			0.594	2.5	4.6	3900

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.22	22.14	77246	4111	99.69	0.12264	0.12128	0.12	0.14838	0.15	RANDOM	9.11

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]
0.95			-0.44		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.141
r_dihedral_angle_4_deg	16.047
r_dihedral_angle_3_deg	13.118
r_sphericity_free	9.432
r_dihedral_angle_1_deg	6.229
r_scangle_it	4.666
r_scbond_it	3.472
r_sphericity_bonded	2.92
r_mcangle_it	2.09
r_mcbond_it	1.924
r_angle_refined_deg	1.84
r_rigid_bond_restr	1.735
r_angle_other_deg	1.047
r_mcbond_other	0.672
r_symmetry_vdw_other	0.331
r_symmetry_hbond_refined	0.317
r_symmetry_vdw_refined	0.282
r_nbd_refined	0.254
r_nbd_other	0.215
r_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.198
r_chiral_restr	0.125
r_nbtor_other	0.094
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1967
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement