6K9Z | pdb_00006k9z

STRUCTURE OF URIDYLYLTRANSFERASE MUTANT

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6K5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG 600, calcium acetate, cacodylate buffer, UDP-Glu

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.188	α = 90
b = 62.188	β = 90
c = 308.594	γ = 120

Symmetry
Space Group	P 32 2 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 QUANTUM 315r		2018-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.78	50	100	0.064	0.069	0.025	6.8	6.8		68099

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.81	100		0.54	0.583	0.214	0.855		6.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6k5z	1.78	47.76	64533	3456	99.94	0.1741	0.173	0.1872	0.1956	0.2084	RANDOM	25.418

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]
0.03	0.02		0.03		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.118
r_dihedral_angle_4_deg	14.702
r_dihedral_angle_3_deg	14.045
r_dihedral_angle_1_deg	7.248
r_angle_refined_deg	1.911
r_angle_other_deg	1.464
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4877
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	60

Software

Software
Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing