1GTK

Time-resolved and static-ensemble structural chemistry of hydroxymethylbilane synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YPNPDB ENTRY 2YPN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.3PROTEIN WAS CRYSTALLISED AT PH 5.3 IN SITTING DROPS OF 0.05 ML WITH 6-7 MG/ML OF PROTEIN, 0.3 MM EDTA, 15 MM DITHIOTHREITOL, 10%(W/V) PEG6000 AND 0.01% NAN3 IN 0.1 M SODIUM ACETATE.
Crystal Properties
Matthews coefficientSolvent content
2.4550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.5α = 90
b = 75.9β = 90
c = 50.1γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD1997-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID09ESRFID09

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6643.858734417
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.7570.7

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 2YPN1.6643.85327081709870.20.1980.247RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.704
r_scbond_it3.14
r_angle_other_deg2.004
r_mcangle_it1.982
r_mcbond_it1.174
r_dihedral_angle_3_deg0.98
r_symmetry_vdw_refined0.304
r_symmetry_vdw_other0.292
r_nbd_refined0.281
r_symmetry_hbond_refined0.262
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.704
r_scbond_it3.14
r_angle_other_deg2.004
r_mcangle_it1.982
r_mcbond_it1.174
r_dihedral_angle_3_deg0.98
r_symmetry_vdw_refined0.304
r_symmetry_vdw_other0.292
r_nbd_refined0.281
r_symmetry_hbond_refined0.262
r_nbd_other0.218
r_xyhbond_nbd_refined0.173
r_xyhbond_nbd_other0.141
r_chiral_restr0.117
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
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_other
r_long_range_B_refined
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 Atoms2228
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
Ophasing