X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62980.1 M sodium acetate, pH 4.6, 30% PEG 400, 100mM protoporphyrin IX disodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.554α = 90
b = 45.213β = 112.11
c = 113.763γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA

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
12.69105.497.10.0958.32.6107672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.692.8597.74.42.1

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 REPLACEMENTTHROUGHOUTPDB entry 2ON72.6914.851047253597.290.294360.292470.33036RANDOM38.218
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]
3.750.85-8.212.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.849
r_dihedral_angle_3_deg15.813
r_dihedral_angle_4_deg11.975
r_dihedral_angle_1_deg5.007
r_long_range_B_refined3.607
r_mcangle_it1.447
r_angle_refined_deg0.971
r_angle_other_deg0.893
r_mcbond_it0.798
r_scbond_it0.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.849
r_dihedral_angle_3_deg15.813
r_dihedral_angle_4_deg11.975
r_dihedral_angle_1_deg5.007
r_long_range_B_refined3.607
r_mcangle_it1.447
r_angle_refined_deg0.971
r_angle_other_deg0.893
r_mcbond_it0.798
r_scbond_it0.557
r_chiral_restr0.055
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3340
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms40

Software

Software
Software NamePurpose
CrysalisProdata collection
PHASERphasing
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling