5GJP

Crystal structure of SrLDC in complex with PLP and Cadaverine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GJN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293PEG 200, Sodium phosphate, NaCl
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.734α = 90
b = 111.734β = 90
c = 112.976γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.97934PAL/PLS7A (6B, 6C1)

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
12.55096.80.13227.824.214439
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5495.10.3170.90712.9

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 REPLACEMENTTHROUGHOUT5GJN2.5501367076696.760.20030.19790.2786RANDOM52.041
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]
1.450.721.45-4.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_4_deg18.14
r_dihedral_angle_3_deg17.295
r_dihedral_angle_1_deg6.892
r_mcangle_it5.361
r_mcbond_it3.547
r_mcbond_other3.546
r_angle_refined_deg1.636
r_angle_other_deg1.015
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.543
r_dihedral_angle_4_deg18.14
r_dihedral_angle_3_deg17.295
r_dihedral_angle_1_deg6.892
r_mcangle_it5.361
r_mcbond_it3.547
r_mcbond_other3.546
r_angle_refined_deg1.636
r_angle_other_deg1.015
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2948
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction