1S07

Crystal Structure of the R253A Mutant of 7,8-Diaminopelargonic Acid Synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherWT dimer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5294PEG4000, MPD, HEPES, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0941.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.08α = 90
b = 56.527β = 96.32
c = 120.993γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2001-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.85EMBL/DESY, HAMBURGBW7B

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
12.422090.60.07714.8297302693634.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.4855.30.02824.8

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTWT dimer2.42202540725407141389.320.190.189680.187760.22414RANDOM28.654
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]
-1.20.482.59-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.18
r_dihedral_angle_1_deg3.93
r_scangle_it3.201
r_scbond_it1.883
r_angle_refined_deg1.654
r_mcangle_it1.316
r_angle_other_deg1.174
r_mcbond_it0.697
r_symmetry_vdw_refined0.476
r_symmetry_vdw_other0.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.18
r_dihedral_angle_1_deg3.93
r_scangle_it3.201
r_scbond_it1.883
r_angle_refined_deg1.654
r_mcangle_it1.316
r_angle_other_deg1.174
r_mcbond_it0.697
r_symmetry_vdw_refined0.476
r_symmetry_vdw_other0.462
r_nbd_refined0.276
r_nbtor_other0.271
r_nbd_other0.218
r_xyhbond_nbd_refined0.171
r_symmetry_hbond_refined0.128
r_xyhbond_nbd_other0.126
r_chiral_restr0.09
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6590
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing