2QCD | pdb_00002qcd

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP

X-RAY DIFFRACTION

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Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.394	α = 90
b = 61.643	β = 112.71
c = 69.97	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	mirors	2006-08-15	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	2.03	42.3	98	0.095	18.6	6.2		34716

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)
	2.03	2.08	83.8		0.344	3.9	4.7	2961

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	2.03	42.26	32963	1733	98.49	0.15174	0.14947	0.1622	0.1946	0.2045	RANDOM	20.797

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]
-0.05		1.47	-1.18		2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.246
r_dihedral_angle_4_deg	15.665
r_dihedral_angle_3_deg	13.817
r_dihedral_angle_1_deg	6.189
r_scangle_it	3.42
r_scbond_it	2.38
r_angle_refined_deg	1.388
r_mcangle_it	1.258
r_mcbond_it	1.175
r_angle_other_deg	0.93
r_symmetry_vdw_other	0.292
r_nbd_refined	0.218
r_nbd_other	0.2
r_symmetry_vdw_refined	0.182
r_mcbond_other	0.182
r_symmetry_hbond_refined	0.18
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.083
r_chiral_restr	0.08
r_bond_refined_d	0.014
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	3943
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	42

Software

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