2R5S

The crystal structure of a domain of protein VP0806 (unknown function) from Vibrio parahaemolyticus RIMD 2210633


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP628920% PEG 8000, 0.1M MES, 0.2M Ca(OAc)2, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4249.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.001α = 90
b = 116.476β = 88.75
c = 62.224γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-08-11MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918, 0.97938APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1429.1295.50.05928.233.4197621976245.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.142.277.30.3782.472.91053

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.1429.121872818728101195.040.226510.226510.223430.27922RANDOM57.175
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]
1.14-0.12-1.620.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.574
r_dihedral_angle_3_deg21.889
r_dihedral_angle_4_deg11.561
r_dihedral_angle_1_deg6.685
r_scangle_it4.501
r_scbond_it2.994
r_angle_refined_deg2.073
r_mcangle_it1.686
r_mcbond_it0.995
r_symmetry_hbond_refined0.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.574
r_dihedral_angle_3_deg21.889
r_dihedral_angle_4_deg11.561
r_dihedral_angle_1_deg6.685
r_scangle_it4.501
r_scbond_it2.994
r_angle_refined_deg2.073
r_mcangle_it1.686
r_mcbond_it0.995
r_symmetry_hbond_refined0.385
r_nbtor_refined0.317
r_symmetry_vdw_refined0.273
r_nbd_refined0.254
r_xyhbond_nbd_refined0.178
r_chiral_restr0.151
r_bond_refined_d0.021
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2712
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
DMphasing
HKL-3000phasing