X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZMDPDB ENTRY 2ZMD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629320 % PEG 300, 0.1 M HEPES, 2.5 % Isopropanol, 5 % Glycerol, 50 mM Ammonium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.98α = 90
b = 104.95β = 90
c = 111.02γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray94IMAGE PLATERIGAKU RAXIS IV++2008-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.740.3697.80.0720.07921.25.711436175.912
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)
12.72.85970.5190.23235.89374

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ZMD2.740.361089054597.440.222880.220720.26457RANDOM45.162
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]
-2.75-0.543.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg24.509
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg5.335
r_angle_refined_deg0.973
r_scangle_it0.858
r_angle_other_deg0.773
r_scbond_it0.557
r_mcangle_it0.53
r_mcbond_it0.484
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.066
r_dihedral_angle_4_deg24.509
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg5.335
r_angle_refined_deg0.973
r_scangle_it0.858
r_angle_other_deg0.773
r_scbond_it0.557
r_mcangle_it0.53
r_mcbond_it0.484
r_nbd_refined0.198
r_symmetry_vdw_other0.193
r_symmetry_vdw_refined0.182
r_symmetry_hbond_refined0.18
r_nbtor_refined0.17
r_nbd_other0.164
r_xyhbond_nbd_refined0.118
r_nbtor_other0.081
r_chiral_restr0.057
r_mcbond_other0.042
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2083
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms47

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling