X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUPPDB ENTRY 1DUP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17DROP: 3.0 MG/ML PROTEIN, 0.05 M IMIDAZOL MALATE BUFFER, PH 7.0, 21% PEG 400, 20 MM SRCL2, 5 MM DUDP; WELL: 0.1 M IMIDAZOLE MALATE BUFFER, PH 7.0, 42% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.4364

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.7α = 90
b = 106.7β = 90
c = 106.7γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMARRESEARCHMIRRORS1995-10-16M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.05251000.1240.12417.710.513598-322.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.091000.6860.6863.810

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 REPLACEMENTFREE RPDB ENTRY 1DUP2.0520135386681000.1680.1670.201RANDOM27.9
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]
27.927.927.9
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.7
p_staggered_tor13.4
p_scangle_it7.8
p_scbond_it6.1
p_planar_tor6.1
p_mcangle_it3.8
p_mcbond_it2.9
p_multtor_nbd0.26
p_chiral_restr0.216
p_singtor_nbd0.19
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor26.7
p_staggered_tor13.4
p_scangle_it7.8
p_scbond_it6.1
p_planar_tor6.1
p_mcangle_it3.8
p_mcbond_it2.9
p_multtor_nbd0.26
p_chiral_restr0.216
p_singtor_nbd0.19
p_xyhbond_nbd0.15
p_planar_d0.041
p_angle_d0.04
p_bond_d0.019
p_plane_restr0.011
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 Atoms919
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms25

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling