X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details 50 mM Bis-Tris, pH 6.5, 18% PEG-3350, 2% tascimate, pH 6.0, 1:100 m/m ratio protein:chymotrypsin, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.86 α = 90
b = 38.86 β = 90
c = 213.31 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-04-14
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.2716, 1.2983 NSLS X29A

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 40 99.5 -- -- -- 5.8 -- 10188 0.0 -3.0 --
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 2.23 98.1 -- -- 5.6 5.8 2879

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 38.27 -- -- 9676 9676 514 99.43 0.21144 0.21144 0.20938 0.25123 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 2.157 642 35 565 0.226 0.294 -- 93.46
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.182
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.779
r_scbond_it 1.695
r_mcangle_it 0.998
r_mcbond_other 0.132
r_mcbond_it 0.551
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.076
r_dihedral_angle_4_deg 16.486
r_dihedral_angle_3_deg 14.372
r_dihedral_angle_2_deg 42.316
r_dihedral_angle_1_deg 6.462
r_angle_other_deg 0.884
r_angle_refined_deg 1.382
r_bond_other_d 0.001
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1316
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 35

Software

Computing
Computing Package Purpose
CBASS Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0072 refinement
Phaser model building
CBASS data collection