7E9V | pdb_00007e9v

The Crystal Structure of human UMP-CMP kinase from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.5M (NH4)2SO4, 0.1M Tris pH8.5

Crystal Properties
Matthews coefficient	Solvent content
2.56	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.926	α = 90
b = 61.926	β = 90
c = 225.397	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2020-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.1	48.473	100	0.075	24	18.1		15960

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	2.1	2.16			0.937

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1TEV	2.1	48.473	15874	818	99.987	0.207	0.205	0.21	0.2497	0.25	48.109

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]
1.072	0.536		1.072		-3.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.577
r_dihedral_angle_4_deg	18.241
r_dihedral_angle_3_deg	17.218
r_lrange_it	8.935
r_lrange_other	8.9
r_scangle_other	7.913
r_scangle_it	7.904
r_dihedral_angle_1_deg	6.073
r_scbond_it	5.315
r_scbond_other	5.314
r_mcangle_it	5.071
r_mcangle_other	5.069
r_mcbond_it	3.973
r_mcbond_other	3.968
r_angle_refined_deg	1.636
r_angle_other_deg	1.401
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.221
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.175
r_nbd_other	0.175
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1528
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing