4Y9O

PA3825-EAL Metal-Free-Apo Structure - Manganese Co-crystallisation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.12770.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic and 0.1 M sodium acetate pH 4.5, 0.2 M Manganese Chloride
Crystal Properties
Matthews coefficientSolvent content
2.448.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.53α = 90
b = 64.53β = 90
c = 134.08γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I021.77DiamondI02

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
11.8158.1599.090.04619.65.92647125106
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)
11.811.85791.710.3132.42.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.8158.1525106129799.090.184960.183360.21551RANDOM29.53
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]
-0.05-0.050.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.618
r_dihedral_angle_4_deg19.79
r_dihedral_angle_3_deg12.014
r_long_range_B_refined6.644
r_long_range_B_other6.599
r_dihedral_angle_1_deg5.18
r_scangle_other4.625
r_scbond_it3.026
r_scbond_other2.999
r_mcangle_it2.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.618
r_dihedral_angle_4_deg19.79
r_dihedral_angle_3_deg12.014
r_long_range_B_refined6.644
r_long_range_B_other6.599
r_dihedral_angle_1_deg5.18
r_scangle_other4.625
r_scbond_it3.026
r_scbond_other2.999
r_mcangle_it2.248
r_mcangle_other2.248
r_mcbond_other1.688
r_mcbond_it1.687
r_angle_refined_deg1.392
r_angle_other_deg0.938
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1995
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing