2I9Z | pdb_00002i9z

Structural Genomics, the Crystal structure of full-length SpoVG from Staphylococcus epidermidis ATCC 12228


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I9XPDB ENTRY 2I9X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62770.2M Ammonium sulfate, 0.1M Sodium acetate, 12%(w/v) PEG4000 , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0740.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.604α = 90
b = 63.604β = 90
c = 98.498γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirror2006-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97932APS19-ID

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
12.344.9999.70.12918.987.294869486
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)
12.32.3897.70.5312.544.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2I9X2.344.998946894649399.70.225330.223240.220.264080.23RANDOM30.262
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.123
r_dihedral_angle_4_deg20.097
r_dihedral_angle_3_deg18.589
r_dihedral_angle_1_deg7.584
r_scangle_it3.514
r_scbond_it2.205
r_mcangle_it1.685
r_angle_refined_deg1.421
r_mcbond_it0.959
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.123
r_dihedral_angle_4_deg20.097
r_dihedral_angle_3_deg18.589
r_dihedral_angle_1_deg7.584
r_scangle_it3.514
r_scbond_it2.205
r_mcangle_it1.685
r_angle_refined_deg1.421
r_mcbond_it0.959
r_nbtor_refined0.296
r_symmetry_hbond_refined0.274
r_nbd_refined0.215
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.133
r_chiral_restr0.1
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms1360
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing