X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 26% PEG 2000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.32 α = 90
b = 55.48 β = 90
c = 72.37 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APEX II CCD -- 2008-10-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE SIEMENS 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.1 36.86 99.5 0.078 0.078 -- 3.5 12150 12085 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.1 2.2 99.5 0.249 0.249 4.1 2.1 1558

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 27.75 -- 0.0 12100 12023 830 99.36 0.216 0.205 0.201 0.271 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.154 -- 60 812 0.218 0.206 -- 99.09
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.957
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.279
r_mcbond_it 0.383
r_dihedral_angle_1_deg 4.225
r_gen_planes_refined 0.003
r_dihedral_angle_4_deg 15.254
r_bond_refined_d 0.007
r_mcangle_it 0.676
r_scbond_it 1.217
r_chiral_restr 0.073
r_symmetry_hbond_refined 0.145
r_scangle_it 1.908
r_nbd_refined 0.201
r_angle_refined_deg 0.994
r_dihedral_angle_3_deg 16.361
r_metal_ion_refined 0.007
r_symmetry_vdw_refined 0.149
r_dihedral_angle_2_deg 43.034
r_xyhbond_nbd_refined 0.145
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1638
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 166

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
APEX data collection
SAINT data reduction
SADABS data scaling
MOLREP phasing