8HRV | pdb_00008hrv

dutpase of helicobacter pylori 26695

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	0.1 M amino acid mix,0.1 M buffer system1 pH 6.5, 50% v/v precipitant mix4

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.869	α = 90
b = 103.869	β = 90
c = 78.651	γ = 120

Symmetry
Space Group	P 63

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 6M		2021-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9805	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	89.95	100	0.129	0.99	18	19.3		32696

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.93

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	59.28	32675	1634	99.988	0.147	0.1447	0.15	0.1812	0.19	23.815

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]
0.467	0.233		0.467		-1.515

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.657
r_dihedral_angle_3_deg	13.271
r_dihedral_angle_2_deg	8.149
r_dihedral_angle_1_deg	6.577
r_lrange_it	6.048
r_lrange_other	6.003
r_scangle_it	4.978
r_scangle_other	4.977
r_scbond_other	3.259
r_scbond_it	3.256
r_mcangle_it	2.824
r_mcangle_other	2.824
r_mcbond_it	1.989
r_mcbond_other	1.985
r_angle_refined_deg	1.442
r_angle_other_deg	0.483
r_symmetry_nbd_refined	0.267
r_nbd_refined	0.221
r_symmetry_nbd_other	0.199
r_chiral_restr_other	0.179
r_nbtor_refined	0.163
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.135
r_ncsr_local_group_2	0.102
r_ncsr_local_group_1	0.1
r_ncsr_local_group_3	0.098
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.071
r_metal_ion_refined	0.039
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3267
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	91

Software

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