4GUL

Study on structure and function relationships in human ferric Pirin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J1L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5289PEG 20000, 0.1 MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.305α = 90
b = 67.031β = 90
c = 107.058γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.80APS22-ID

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
11.821.8894.30.14932.939.62732825931
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8467.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1J1L1.821.872732825931139794.30.18960.18710.2337RANDOM21.715
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]
-13.4612.560.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.097
r_dihedral_angle_4_deg21.617
r_dihedral_angle_3_deg14.356
r_dihedral_angle_1_deg6.863
r_angle_refined_deg2.265
r_angle_other_deg0.999
r_chiral_restr0.157
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.097
r_dihedral_angle_4_deg21.617
r_dihedral_angle_3_deg14.356
r_dihedral_angle_1_deg6.863
r_angle_refined_deg2.265
r_angle_other_deg0.999
r_chiral_restr0.157
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2250
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms1

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing