X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.005 M BIS TRIS, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (20-25% PEG 8K, 0.10 M PIPES PH 6.5) CRYSTALS SOAKED FOR 60 MINUTES IN WELL SOLUTION WITH 0.005 M magnesium chloride, 0.005 M UMP, temperature 277K, VAPOR DIFFUSION, HANGING DROP, pH 6.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 134.01 α = 90
b = 134.01 β = 90
c = 39.09 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-11-30
Diffraction Radiation
Monochromator Protocol
SI 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM -- APS 8-BM

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 50 98.9 0.071 -- -- 3.8 -- 45396 -- -- --
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 2.15 97.6 0.342 -- 3.42 3.2 --

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 32.19 -- -- -- 45392 2257 98.9 -- 0.153 0.15 0.198 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 2.15 -- 157 3184 0.195 0.278 -- 97.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.09
Anisotropic B[1][1] -0.155
Anisotropic B[1][2] -0.078
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.155
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.233
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.043
r_angle_refined_deg 1.316
r_symmetry_vdw_refined 0.204
r_mcangle_it 1.918
r_nbtor_refined 0.304
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 5.492
r_symmetry_hbond_refined 0.178
r_scbond_it 3.867
r_mcbond_it 1.141
r_dihedral_angle_2_deg 39.322
r_dihedral_angle_4_deg 20.609
r_nbd_refined 0.193
r_dihedral_angle_3_deg 14.187
r_bond_refined_d 0.015
r_xyhbond_nbd_refined 0.172
r_chiral_restr 0.093
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4652
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 848

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.701
MOLREP phasing