4I45

Crystal Structure of Orf6 protein from Photobacterium profundum, Mg2+-bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.05 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9837.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.292α = 90
b = 54.362β = 90
c = 88.363γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.000ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.446.396.32473623821
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4576.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3R871.446.32260622606121596.30.150520.14820.19606RANDOM17.875
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]
-1.49-0.872.36
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.03
r_dihedral_angle_2_deg32.227
r_sphericity_bonded19.171
r_dihedral_angle_4_deg14.692
r_dihedral_angle_3_deg12.263
r_dihedral_angle_1_deg6.499
r_rigid_bond_restr2.951
r_angle_refined_deg1.608
r_angle_other_deg0.903
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.03
r_dihedral_angle_2_deg32.227
r_sphericity_bonded19.171
r_dihedral_angle_4_deg14.692
r_dihedral_angle_3_deg12.263
r_dihedral_angle_1_deg6.499
r_rigid_bond_restr2.951
r_angle_refined_deg1.608
r_angle_other_deg0.903
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1055
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms1

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling