2QCE | pdb_00002qce

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to sulfate, glycerol, and chloride

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
2.47	50.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.224	α = 90
b = 116.912	β = 90
c = 61.965	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		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	1.42	34.8	84.4	0.079	21	6.7		45102

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	1.42	1.47	26.3		0.263	0.492	1.7	2.4	1381

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	1.43	34.79	42806	2295	86.41	0.14603	0.14504	0.1531	0.16485	0.1717	RANDOM	10.86

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]
1.23			-0.6		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.879
r_dihedral_angle_4_deg	14.822
r_dihedral_angle_3_deg	12.673
r_dihedral_angle_1_deg	5.591
r_scangle_it	2.856
r_scbond_it	1.991
r_angle_refined_deg	1.238
r_mcangle_it	0.991
r_mcbond_it	0.934
r_angle_other_deg	0.88
r_symmetry_vdw_other	0.255
r_nbd_refined	0.225
r_nbd_other	0.197
r_symmetry_vdw_refined	0.191
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.157
r_mcbond_other	0.156
r_nbtor_other	0.082
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1964
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
COMO	phasing