X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.3
Temperature 291.0
Details 25% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium acetate. Chymotrypsin was added to the crystallization sample at a molar ratio of approx. 1:100, pH 7.3, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.09 α = 90
b = 80.1 β = 90
c = 42.74 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2007-12-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97242 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
1.85 40 100.0 0.133 -- -- 11.4 -- 17895 -- -- --
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)
1.85 1.92 99.9 0.656 -- -- 10.1 1744

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 1.85 30.0 -- 0.0 -- 17560 883 99.57 0.187 0.187 0.185 0.226 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 1.85 1.898 -- 69 1185 0.206 0.289 -- 99.13
X Ray Diffraction 1.898 1.95 -- 75 1178 0.198 0.246 -- 99.444
X Ray Diffraction 1.95 2.006 -- 66 1131 0.189 0.229 -- 99.833
X Ray Diffraction 2.006 2.067 -- 59 1125 0.178 0.247 -- 99.831
X Ray Diffraction 2.067 2.135 -- 65 1068 0.175 0.245 -- 99.736
X Ray Diffraction 2.135 2.209 -- 55 1037 0.175 0.199 -- 99.635
X Ray Diffraction 2.209 2.292 -- 42 1028 0.164 0.252 -- 99.535
X Ray Diffraction 2.292 2.385 -- 45 994 0.178 0.234 -- 99.712
X Ray Diffraction 2.385 2.491 -- 49 930 0.175 0.244 -- 99.391
X Ray Diffraction 2.491 2.611 -- 54 888 0.185 0.253 -- 99.158
X Ray Diffraction 2.611 2.751 -- 33 871 0.196 0.271 -- 99.559
X Ray Diffraction 2.751 2.917 -- 49 812 0.188 0.205 -- 99.538
X Ray Diffraction 2.917 3.116 -- 33 777 0.194 0.215 -- 99.143
X Ray Diffraction 3.116 3.363 -- 36 727 0.193 0.232 -- 99.739
X Ray Diffraction 3.363 3.679 -- 33 666 0.189 0.205 -- 99.431
X Ray Diffraction 3.679 4.106 -- 23 622 0.173 0.229 -- 99.845
X Ray Diffraction 4.106 4.726 -- 30 552 0.145 0.17 -- 99.828
X Ray Diffraction 4.726 5.753 -- 26 464 0.202 0.225 -- 99.796
X Ray Diffraction 5.753 7.99 -- 28 375 0.234 0.253 -- 100.0
X Ray Diffraction 7.99 30.0 -- 13 247 0.222 0.179 -- 99.617
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.434
Anisotropic B[1][1] -0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.18
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.38
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 14.033
r_nbd_refined 0.195
r_nbtor_other 0.084
r_mcangle_it 3.225
r_mcbond_it 2.551
r_bond_other_d 0.001
r_dihedral_angle_3_deg 12.409
r_dihedral_angle_2_deg 34.249
r_gen_planes_refined 0.005
r_xyhbond_nbd_refined 0.123
r_chiral_restr 0.089
r_gen_planes_other 0.001
r_angle_other_deg 0.921
r_nbtor_refined 0.17
r_symmetry_vdw_refined 0.072
r_mcbond_other 0.685
r_scbond_it 2.626
r_nbd_other 0.17
r_scangle_it 3.559
r_dihedral_angle_1_deg 5.324
r_angle_refined_deg 1.344
r_symmetry_vdw_other 0.232
r_symmetry_hbond_refined 0.136
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1493
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 97

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: refmac_5.3.0037
PDB_EXTRACT data extraction version: 2.000
ADSC data collection version: Quantum
ARP/wARP model building
Coot model building
MolProbity model building