2QCL | pdb_00002qcl

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

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
2.44	49.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.493	α = 90
b = 61.596	β = 113.58
c = 70.305	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	IMAGE PLATE	MAR scanner 345 mm plate		2006-08-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5419

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	1.85	26	97.2	0.062	20	3.8		45421

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	1.85	1.92	85.5		0.286	3.4	2.9	3963

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	1.85	26	43118	2268	97.32	0.17391	0.17185	0.18	0.21278	0.22	RANDOM	24.202

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]
1.18		2.07	-1.16		1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.105
r_dihedral_angle_4_deg	14.775
r_dihedral_angle_3_deg	14.137
r_dihedral_angle_1_deg	5.995
r_scangle_it	3.606
r_scbond_it	2.449
r_angle_refined_deg	1.498
r_mcangle_it	1.275
r_mcbond_it	1.182
r_angle_other_deg	0.961
r_symmetry_vdw_other	0.311
r_symmetry_hbond_refined	0.234
r_mcbond_other	0.223
r_nbd_refined	0.214
r_nbd_other	0.204
r_nbtor_refined	0.174
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.088
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
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	3917
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement