4R7K | pdb_00004r7k

1.88 Angstrom Resolution Crystal Structure of Hypothetical Protein jhp0584 from Helicobacter pylori.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	Protein: 7.7 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME; Screen: PACT (G11), 0.1M MMT buffer (pH 9.0), 25%(w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.832	α = 90
b = 70.945	β = 91.67
c = 86.454	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	MARMOSAIC 300 mm CCD	Beryllium lenese	2014-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97892	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.88	30	99.7	0.081	0.081	24.3	4.1	66450	66450		-3	27.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.88	1.91	100		0.534	0.534	2.6	4.2	3305

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	1.88	27.43	63040	63040	3360	99.35	0.17268	0.17268	0.17084	0.183	0.20746	0.2146	RANDOM	34.992

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]
0.22		-0.11	-0.8		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.288
r_dihedral_angle_4_deg	19.483
r_dihedral_angle_3_deg	9.133
r_long_range_B_refined	6.215
r_long_range_B_other	6.125
r_scangle_other	3.977
r_dihedral_angle_1_deg	3.53
r_scbond_it	2.666
r_scbond_other	2.662
r_mcangle_it	2.361
r_mcangle_other	2.361
r_mcbond_other	1.638
r_mcbond_it	1.637
r_angle_refined_deg	1.495
r_angle_other_deg	0.708
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5544
Nucleic Acid Atoms
Solvent Atoms	448
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing