X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CD1PDB Entry 1CD1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.3277PEG 4000, calcium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.4249.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.451α = 90
b = 77.045β = 107.63
c = 111.014γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 3152004-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9537ALS8.2.2

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
12.2500.07520.82.448471
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2586.90.372

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1CD12.239.684401444014141493.720.243210.241560.29368RANDOM71.352
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]
-0.010.02-0.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.895
r_dihedral_angle_4_deg22.531
r_dihedral_angle_3_deg17.989
r_dihedral_angle_1_deg5.792
r_scangle_it2.552
r_angle_refined_deg1.848
r_scbond_it1.757
r_mcangle_it1.135
r_mcbond_it0.737
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.895
r_dihedral_angle_4_deg22.531
r_dihedral_angle_3_deg17.989
r_dihedral_angle_1_deg5.792
r_scangle_it2.552
r_angle_refined_deg1.848
r_scbond_it1.757
r_mcangle_it1.135
r_mcbond_it0.737
r_nbtor_refined0.313
r_nbd_refined0.232
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.179
r_chiral_restr0.149
r_bond_refined_d0.015
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5911
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms214

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
MOLREPphasing