2QCC

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase, apo form

X-RAY DIFFRACTION

---

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.019	α = 90
b = 75.912	β = 90
c = 119.545	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	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 Merge 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	47	94.3	0.094	28.5	10.8		46969

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	1.84	1.91	58.8		0.619	2	6.6	2878

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	46.96	44555	2352	96.01	0.2	0.19705	0.25755	RANDOM	34.791

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]
-1.28			2.54		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.317
r_dihedral_angle_3_deg	14.829
r_dihedral_angle_4_deg	11.271
r_dihedral_angle_1_deg	5.862
r_scangle_it	2.775
r_scbond_it	1.908
r_angle_refined_deg	1.281
r_mcangle_it	1.08
r_angle_other_deg	0.886
r_mcbond_it	0.696
r_symmetry_vdw_other	0.298
r_nbd_refined	0.21
r_nbd_other	0.192
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.18
r_mcbond_other	0.18
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.086
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.052
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3814
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	22

Software

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