2I9C

Crystal Structure of the Protein RPA1889 from Rhodopseudomonas palustris CGA009


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72935% Tascimate, 10% PEG5000 MME, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.022α = 90
b = 78.022β = 90
c = 38.979γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32006-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97904APS19-BM

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
1267.5799.70.0660.057794849449-330.3
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)
122.021000.2990.2986.837.1206

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT233.799449898945199.730.176030.174720.20189RANDOM33.113
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]
0.860.430.86-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.018
r_dihedral_angle_3_deg13.601
r_dihedral_angle_4_deg13.223
r_dihedral_angle_1_deg6.365
r_scangle_it4.779
r_scbond_it3.622
r_angle_refined_deg1.605
r_mcangle_it1.558
r_mcbond_it1.254
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.018
r_dihedral_angle_3_deg13.601
r_dihedral_angle_4_deg13.223
r_dihedral_angle_1_deg6.365
r_scangle_it4.779
r_scbond_it3.622
r_angle_refined_deg1.605
r_mcangle_it1.558
r_mcbond_it1.254
r_nbtor_refined0.297
r_symmetry_hbond_refined0.223
r_symmetry_vdw_refined0.214
r_nbd_refined0.202
r_xyhbond_nbd_refined0.155
r_chiral_restr0.101
r_bond_refined_d0.02
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 Atoms929
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
CCP4phasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
Omodel building