3DCA

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.2M AMMONIUM SULPHATE, 0.1M NA CACODILATE PH6.5, 30%PEG8K, , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
6.5881.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 193.495α = 90
b = 193.495β = 90
c = 118.848γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRROR2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.3536.5993.60.0880.08813.71622225622256-398.16
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)RedundancyNumber Unique Reflections (All)
3.353.4793.20.4260.4261.522257

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 DIFFRACTIONSADTHROUGHOUT3.3536.592214722147113392.990.2740.2740.2730.29RANDOM30.57
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]
0.120.060.12-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg20.579
r_dihedral_angle_3_deg17.871
r_dihedral_angle_1_deg6.695
r_angle_other_deg4.25
r_angle_refined_deg1.685
r_chiral_restr0.073
r_bond_refined_d0.017
r_gen_planes_other0.012
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.406
r_dihedral_angle_4_deg20.579
r_dihedral_angle_3_deg17.871
r_dihedral_angle_1_deg6.695
r_angle_other_deg4.25
r_angle_refined_deg1.685
r_chiral_restr0.073
r_bond_refined_d0.017
r_gen_planes_other0.012
r_gen_planes_refined0.009
r_bond_other_d
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3864
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms30

Software

Software
Software NamePurpose
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
MAINmodel building
REFMACrefinement
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
DMphasing
MAINphasing
MAINrefinement
Cootmodel building