2GZ1

Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from Streptococcus pneumoniae complexed with NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GYYPDB Entry: 2GYY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629350 mM Citrate pH 6.0 200 mM ammonium acetate 20% PEG 8000 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4148.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.709α = 90
b = 99.165β = 100.83
c = 64.525γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.839.5399.90.05411.43.64682266822622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.861000.3143.53.556788

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 REPLACEMENTTHROUGHOUTPDB Entry: 2GYY1.839.536821668216345299.890.1620.1620.160.191RANDOM12.539
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.026
r_scangle_it2.513
r_scbond_it1.554
r_angle_refined_deg1.262
r_mcangle_it0.809
r_angle_other_deg0.777
r_mcbond_it0.408
r_nbd_other0.245
r_symmetry_vdw_other0.225
r_nbd_refined0.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.026
r_scangle_it2.513
r_scbond_it1.554
r_angle_refined_deg1.262
r_mcangle_it0.809
r_angle_other_deg0.777
r_mcbond_it0.408
r_nbd_other0.245
r_symmetry_vdw_other0.225
r_nbd_refined0.192
r_symmetry_hbond_refined0.176
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.161
r_nbtor_other0.08
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5440
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms96

Software

Software
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction