4KIA

Crystal structure of LmHde, heme-degrading enzyme, from Listeria monocytogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FEZPDB ENTRY 3FEZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.628725% PEG 3350, 0.1M sodium citrate, 0.2M ammonium sulfate, pH 5.6, MICROBATCH, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
1.8132.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.61α = 90
b = 59.474β = 94.57
c = 45.434γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315r2009-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7550990.06430.413.61434414209
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)
11.751.81940.1650.1665.783

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 REPLACEMENTCOOT and PROCHECKPDB ENTRY 3FEZ1.7545.29142091347971399.060.191010.188280.24432RANDOM16.237
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]
-0.010.04-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.055
r_dihedral_angle_3_deg12.699
r_dihedral_angle_4_deg7.734
r_sphericity_free5.835
r_dihedral_angle_1_deg5.761
r_scangle_it4.733
r_scbond_it3.213
r_sphericity_bonded3.146
r_mcangle_it2.023
r_rigid_bond_restr1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.055
r_dihedral_angle_3_deg12.699
r_dihedral_angle_4_deg7.734
r_sphericity_free5.835
r_dihedral_angle_1_deg5.761
r_scangle_it4.733
r_scbond_it3.213
r_sphericity_bonded3.146
r_mcangle_it2.023
r_rigid_bond_restr1.98
r_angle_refined_deg1.346
r_mcbond_it1.17
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1253
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
DMmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing