5MJW

Structure of Psb29 at 1.55A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.2M sodium malonate, pH 7, 20% w/v/ PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.5365.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.85α = 90
b = 86.61β = 90
c = 116.02γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

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
12.4755.2699.640.0626.28936.3411662
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)
12.472.5398.770.830.676.45

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MJO2.4755.261110655599.60.219130.21760.24978RANDOM75.277
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]
0.32.42-2.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.098
r_dihedral_angle_4_deg17.445
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg5.205
r_long_range_B_refined2.963
r_long_range_B_other2.962
r_mcangle_it1.687
r_mcangle_other1.687
r_scangle_other1.595
r_angle_refined_deg1.191
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.098
r_dihedral_angle_4_deg17.445
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg5.205
r_long_range_B_refined2.963
r_long_range_B_other2.962
r_mcangle_it1.687
r_mcangle_other1.687
r_scangle_other1.595
r_angle_refined_deg1.191
r_mcbond_it1.011
r_mcbond_other1.011
r_angle_other_deg0.932
r_scbond_it0.925
r_scbond_other0.925
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1578
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing