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 = 38.74 α = 90
b = 38.74 β = 90
c = 214.53 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 -- 2012-03-26
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 1.0750 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
1.75 40 96.6 -- -- -- 6.8 17619 17027 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)
1.75 1.85 98.3 -- -- 5.8 6.9 --

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 1.75 38.12 -- -- 16154 16154 862 97.1 -- 0.175 0.174 0.197 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 1.75 1.8 -- 65 1143 0.249 0.252 -- 97.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.023
Anisotropic B[1][1] -0.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.257
r_scbond_it 1.92
r_mcangle_it 1.242
r_mcbond_other 0.159
r_mcbond_it 0.643
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.077
r_dihedral_angle_4_deg 11.452
r_dihedral_angle_3_deg 12.31
r_dihedral_angle_2_deg 40.149
r_dihedral_angle_1_deg 5.851
r_angle_other_deg 0.832
r_angle_refined_deg 1.281
r_bond_other_d 0.001
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1327
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 105

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