6BA0 | pdb_00006ba0

Pyrimidine-specific Ribonucleoside Hydrolase from Gardnerella vaginalis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	290	0.1M Sodium Acetate 0.2M Ammonium Sulfate 20% (w/v) PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.07	α = 90
b = 79.36	β = 99.62
c = 115.99	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 QUANTUM 210r		2017-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.03	61.87	99.9	0.198	0.213	0.079	0.992	8.5	7.1		96089

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	2.03	2.06	99.2		0.942	1.021	0.387	0.648		6.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MAS	2.03	61.87	91261	4802	99.83	0.1879	0.1863	0.1962	0.2184	0.2263	RANDOM	19.57

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]
0.61		0.36	-0.41		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.197
r_dihedral_angle_4_deg	20.645
r_dihedral_angle_3_deg	12.528
r_dihedral_angle_1_deg	5.642
r_angle_refined_deg	1.387
r_angle_other_deg	0.948
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9396
Nucleic Acid Atoms
Solvent Atoms	862
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction