X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 294.0
Details 0.1 M Hepes 7.5, 0.2 M NaCl, 25% PEG3350 plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.19 α = 90
b = 47.19 β = 90
c = 237.1 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 mirrors 2008-12-17
Diffraction Radiation
Monochromator Protocol
SI-111 CHANNEL MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID

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
2.3 40.29 97.9 0.077 -- -- 5.5 26308 25761 -- -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)
2.3 2.38 82.9 0.301 -- 3.5 4.3 --

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 2.3 40.29 -- -- -- 24379 1283 97.85 -- 0.19244 0.18993 0.23994 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 2.3 2.361 -- 84 1527 0.284 0.312 -- 80.23
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.813
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] -0.01
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_nbd_refined 0.228
r_chiral_restr 0.11
r_bond_refined_d 0.015
r_symmetry_hbond_refined 0.1
r_xyhbond_nbd_refined 0.145
r_angle_refined_deg 1.547
r_mcbond_it 0.603
r_dihedral_angle_3_deg 17.901
r_nbtor_refined 0.317
r_dihedral_angle_4_deg 20.051
r_scangle_it 3.036
r_gen_planes_refined 0.006
r_scbond_it 2.109
r_mcangle_it 1.117
r_symmetry_vdw_refined 0.254
r_dihedral_angle_2_deg 38.18
r_dihedral_angle_1_deg 6.969
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5045
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 76

Software

Software
Software Name Purpose
SBC-Collect data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
HKL-3000 data reduction
HKL-2000 data scaling