1IOV

COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DLN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5AMMONIUM SULFATE, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
237.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.6α = 90
b = 51β = 90
c = 51.2γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295AREA DETECTORSIEMENS1995-11-01M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
12.2750.0678.811579
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.439

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2DLN2.21537591750.1560.20410.3
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
p_staggered_tor22.5
p_transverse_tor19.6
p_angle_d1.1
p_planar_tor1.1
p_mcangle_it0.472
p_xyhbond_nbd0.365
p_scangle_it0.356
p_multtor_nbd0.305
p_mcbond_it0.263
p_singtor_nbd0.204
RMS Deviations
KeyRefinement Restraint Deviation
p_staggered_tor22.5
p_transverse_tor19.6
p_angle_d1.1
p_planar_tor1.1
p_mcangle_it0.472
p_xyhbond_nbd0.365
p_scangle_it0.356
p_multtor_nbd0.305
p_mcbond_it0.263
p_singtor_nbd0.204
p_scbond_it0.197
p_chiral_restr0.115
p_planar_d0.019
p_bond_d0.008
p_plane_restr0.005
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2293
Nucleic Acid Atoms27
Solvent Atoms263
Heterogen Atoms17

Software

Software
Software NamePurpose
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling