2EAW | pdb_00002eaw

Human UMP Synthase (C-terminal Domain- Orotidine 5'-Monophosphate Decarboxylase)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.4	293	2.28M Ammonium sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.571	α = 90
b = 59.37	β = 114.3
c = 69.863	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	BRUKER SMART 6000		2007-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.88	63.67	97.8	0.1414	0.171	4.29	1.84	11598	11348

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)
	2.88	2.9	28.9		0.4	0.5454	2.04	0.49	232

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1DQW	2.88	63.63	11029	10398	522	94.28	0.26179	0.26179	0.25946	0.2577	0.30737	0.2968	RANDOM	10.041

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]
2.07		2.38	-1.84		1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.917
r_dihedral_angle_3_deg	19.021
r_dihedral_angle_4_deg	18.059
r_dihedral_angle_1_deg	8.528
r_scangle_it	3.588
r_scbond_it	2.12
r_angle_refined_deg	1.993
r_mcangle_it	1.326
r_mcbond_it	0.892
r_symmetry_hbond_refined	0.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.917
r_dihedral_angle_3_deg	19.021
r_dihedral_angle_4_deg	18.059
r_dihedral_angle_1_deg	8.528
r_scangle_it	3.588
r_scbond_it	2.12
r_angle_refined_deg	1.993
r_mcangle_it	1.326
r_mcbond_it	0.892
r_symmetry_hbond_refined	0.356
r_nbtor_refined	0.343
r_symmetry_vdw_refined	0.337
r_chiral_restr	0.32
r_nbd_refined	0.274
r_xyhbond_nbd_refined	0.171
r_bond_refined_d	0.025
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3916
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

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.