2VA1

Crystal structure of UMP kinase from Ureaplasma parvum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M AMMONIUM FLUORIDE, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.753	α = 90
b = 96.552	β = 105.75
c = 96.27	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	ADSC CCD	TOROIDAL FOCUSING MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.5	33.42	99.9	0.12	11.4	3.8		48558		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	99.9		0.12	3.1	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 2A1F	2.5	20	46149	2456	99.9	0.235	0.232	0.285	RANDOM	34.56

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]
-0.31		0.92	0.09		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.49
r_dihedral_angle_3_deg	18.484
r_dihedral_angle_4_deg	14.157
r_dihedral_angle_1_deg	5.077
r_scangle_it	1.233
r_angle_refined_deg	1.038
r_mcangle_it	0.754
r_scbond_it	0.75
r_mcbond_it	0.5
r_nbtor_refined	0.292
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.122
r_symmetry_hbond_refined	0.074
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10600
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing