X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 12.2 MG/ML REDUCTIVELY METHYLATED PROTEIN, 2.03 M AMMONIUM SULFATE, 0.100 M MES/ACETATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.87 α = 90
b = 55.87 β = 90
c = 147.34 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm bent cylindrical Si-mirror (Rh coating) 2004-10-24
Diffraction Radiation
Monochromator Protocol
Diamond (111) double-crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 0.97919, 0.97942, 0.95653 APS 14-ID-B

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
1.8 27.45 98.9 0.037 -- -- 13.6 -- 25282 -- -- --
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)
1.8 1.84 99.6 0.123 -- 10.84 10.9 --

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
MAD 1.8 49.088 -- -- -- 25171 1282 98.629 0.184 0.184 0.1817 0.228 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 1.8 1.847 -- 96 1719 0.205 0.3 -- 99.398
X Ray Diffraction 1.847 1.897 -- 87 1705 0.18 0.236 -- 99.28
X Ray Diffraction 1.897 1.952 -- 97 1598 0.184 0.235 -- 97.302
X Ray Diffraction 1.952 2.012 -- 85 1634 0.178 0.238 -- 99.826
X Ray Diffraction 2.012 2.078 -- 78 1592 0.167 0.23 -- 99.94
X Ray Diffraction 2.078 2.151 -- 76 1531 0.17 0.222 -- 99.876
X Ray Diffraction 2.151 2.232 -- 83 1459 0.18 0.22 -- 99.484
X Ray Diffraction 2.232 2.323 -- 67 1389 0.181 0.203 -- 97.391
X Ray Diffraction 2.323 2.426 -- 75 1379 0.177 0.222 -- 99.931
X Ray Diffraction 2.426 2.544 -- 60 1312 0.183 0.197 -- 100.0
X Ray Diffraction 2.544 2.681 -- 86 1217 0.184 0.263 -- 100.0
X Ray Diffraction 2.681 2.843 -- 68 1185 0.194 0.216 -- 100.0
X Ray Diffraction 2.843 3.039 -- 66 1109 0.178 0.241 -- 99.915
X Ray Diffraction 3.039 3.281 -- 59 1047 0.181 0.205 -- 99.91
X Ray Diffraction 3.281 3.593 -- 47 969 0.166 0.23 -- 99.902
X Ray Diffraction 3.593 4.014 -- 53 878 0.162 0.234 -- 99.043
X Ray Diffraction 4.014 4.63 -- 38 777 0.16 0.192 -- 97.839
X Ray Diffraction 4.63 5.658 -- 27 649 0.188 0.166 -- 94.282
X Ray Diffraction 5.658 7.949 -- 21 519 0.231 0.283 -- 94.406
X Ray Diffraction 7.949 49.088 -- 13 221 0.319 0.414 -- 65.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.655
Anisotropic B[1][1] 0.767
Anisotropic B[1][2] 0.384
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.767
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.151
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.527
r_dihedral_angle_3_deg 13.068
r_xyhbond_nbd_refined 0.177
r_mcbond_it 2.086
r_symmetry_hbond_refined 0.184
r_scbond_it 5.903
r_chiral_restr 0.148
r_gen_planes_refined 0.009
r_symmetry_vdw_refined 0.245
r_angle_refined_deg 1.689
r_scangle_it 8.572
r_nbtor_refined 0.313
r_bond_refined_d 0.019
r_nbd_refined 0.212
r_dihedral_angle_1_deg 5.161
r_dihedral_angle_2_deg 39.755
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1803
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 252

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS phasing
REFMAC refinement version: refmac_5.2.0005