X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DGDDIALKYLGLYCINE DECARBOXYLASE, PDB ENTRY 1DGD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.8pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.7847

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.3α = 90
b = 116.3β = 90
c = 190γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATE AREA DETECTORMARRESEARCH1993-10-22M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
12.53099.90.0825.452220

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT AND NON-CRYSTALLOGRAPHIC AVERAGINGTHROUGHOUTDIALKYLGLYCINE DECARBOXYLASE, PDB ENTRY 1DGD2.53824962095.30.1850.1850.235RANDOM19.8
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
x_dihedral_angle_d24.7
x_scangle_it8
x_mcangle_it6.4
x_scbond_it5.4
x_mcbond_it4.2
x_improper_angle_d1.8
x_angle_deg1.7
x_bond_d0.014
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d24.7
x_scangle_it8
x_mcangle_it6.4
x_scbond_it5.4
x_mcbond_it4.2
x_improper_angle_d1.8
x_angle_deg1.7
x_bond_d0.014
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9483
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms45

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MARXDSdata reduction
CCP4data scaling
X-PLORphasing