X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.95 α = 90
b = 139.49 β = 90
c = 182.58 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 FOCUSING MIRRORS 2009-12-15
Diffraction Radiation
Monochromator Protocol
SI(111) DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 1.07188 APS 24-ID-C

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
2.35 50 98.6 0.153 -- -- 4.1 47535 47535 -- -- --
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)
2.35 2.39 98.7 0.862 0.862 2.0 4.0 2335

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 2.35 43.69 -- 0.0 -- 47496 2377 98.31 -- 0.186 0.184 0.237 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 2.347 2.408 -- 165 3162 0.398 0.447 -- 94.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.302
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.248
r_mcbond_it 2.807
r_bond_other_d 0.001
r_mcangle_it 4.612
r_dihedral_angle_2_deg 36.554
r_dihedral_angle_3_deg 13.522
r_gen_planes_other 0.001
r_scbond_it 7.277
r_angle_refined_deg 1.172
r_gen_planes_refined 0.004
r_scangle_it 10.178
r_dihedral_angle_4_deg 13.385
r_chiral_restr 0.066
r_angle_other_deg 0.813
r_bond_refined_d 0.008
r_mcbond_other 0.949
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6241
Nucleic Acid Atoms 0
Heterogen Atoms 239
Solvent Atoms 552

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.5.0070
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data reduction
AMoRE phasing