5FVE | pdb_00005fve

Crystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RKI	PDB ENTRY 4RKI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20% V/V PEG MME550, 6% W/V PEG 20000, 0.01M MGCL2, 0.1M MOPS/HEPES-NA PH 7.3, 0.2M AMMONIUM CITRATE

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.071	α = 90
b = 66.383	β = 115.43
c = 82.778	γ = 90

Symmetry
Space Group	C 1 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	287	CCD	MARRESEARCH		2015-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.07	50	98.5	0.06	33.17	6.8		26589		0.3

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	2.07	50	90.9		0.42	3	5.8

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	PDB ENTRY 4RKI	2.07	74.76	25206	1342	98.53	0.21446	0.2127	0.22	0.24732	0.25	RANDOM	49.506

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]
3.28		2.23	-3.52		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.599
r_dihedral_angle_4_deg	15.393
r_dihedral_angle_3_deg	15.093
r_dihedral_angle_1_deg	6.761
r_long_range_B_refined	4.19
r_long_range_B_other	4.141
r_mcangle_it	2.461
r_mcangle_other	2.461
r_scangle_other	2.34
r_mcbond_it	1.427
r_mcbond_other	1.427
r_scbond_it	1.355
r_scbond_other	1.355
r_angle_refined_deg	1.276
r_angle_other_deg	0.848
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2870
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
CCP4	phasing