X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.6 M sodium chloride, 0.1 M MES pH 6.5, 20 %(w/v) PEG-4000, 5 mM Penicillin G, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.06 α = 90
b = 79.21 β = 90
c = 133.31 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2013-03-13
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97924 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
1.5 50 99.9 -- 0.072 -- 7.1 67683 67683 0.0 0.0 12.89
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)
1.5 1.53 100.0 -- 0.738 4.0 6.1 3327

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 1.495 37.966 -- 0.0 67087 67087 3391 98.87 0.145 0.145 0.143 0.18 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 1.4952 1.5166 2304 118 2186 0.152 0.2053 -- 83.0
X Ray Diffraction 1.5166 1.5392 2593 118 2475 0.1442 0.182 -- 94.0
X Ray Diffraction 1.5392 1.5633 2762 144 2618 0.1436 0.1977 -- 98.0
X Ray Diffraction 1.5633 1.5889 2743 120 2623 0.1422 0.2074 -- 99.0
X Ray Diffraction 1.5889 1.6163 2805 131 2674 0.1387 0.1847 -- 100.0
X Ray Diffraction 1.6163 1.6457 2790 140 2650 0.1336 0.1916 -- 100.0
X Ray Diffraction 1.6457 1.6774 2766 127 2639 0.1387 0.1808 -- 100.0
X Ray Diffraction 1.6774 1.7116 2803 144 2659 0.1406 0.2 -- 100.0
X Ray Diffraction 1.7116 1.7488 2785 132 2652 0.1374 0.2018 -- 100.0
X Ray Diffraction 1.7488 1.7895 2826 157 2669 0.1266 0.2104 -- 100.0
X Ray Diffraction 1.7895 1.8343 2805 149 2656 0.1272 0.1592 -- 100.0
X Ray Diffraction 1.8343 1.8839 2826 155 2671 0.1237 0.1683 -- 100.0
X Ray Diffraction 1.8839 1.9393 2792 135 2657 0.1241 0.1525 -- 100.0
X Ray Diffraction 1.9393 2.0019 2784 173 2611 0.1247 0.161 -- 100.0
X Ray Diffraction 2.0019 2.0734 2838 173 2665 0.1332 0.1773 -- 100.0
X Ray Diffraction 2.0734 2.1564 2823 151 2672 0.1343 0.1735 -- 100.0
X Ray Diffraction 2.1564 2.2546 2809 145 2664 0.132 0.163 -- 100.0
X Ray Diffraction 2.2546 2.3734 2831 153 2678 0.1401 0.1764 -- 100.0
X Ray Diffraction 2.3734 2.5221 2849 146 2703 0.1469 0.1697 -- 100.0
X Ray Diffraction 2.5221 2.7168 2845 141 2704 0.1534 0.1809 -- 100.0
X Ray Diffraction 2.7168 2.9901 2873 132 2741 0.1566 0.1803 -- 100.0
X Ray Diffraction 2.9901 3.4225 2876 133 2743 0.1524 0.1897 -- 100.0
X Ray Diffraction 3.4225 4.311 2941 132 2809 0.1377 0.1566 -- 100.0
X Ray Diffraction 4.311 37.978 3019 142 2877 0.1676 0.2133 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 19.6
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.043
f_plane_restr 0.005
f_bond_d 0.006
f_dihedral_angle_d 14.895
f_angle_d 1.071
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3552
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 370

Software

Software
Software Name Purpose
SBC-Collect data collection
HKL-3000 data collection
HKL-3000 phasing
MOLREP phasing
PHENIX refinement version: (phenix.refine: dev_1745)
HKL-3000 data reduction
HKL-3000 data scaling