X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.15 α = 90
b = 47.59 β = 104.84
c = 42.63 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2000-06-02
Diffraction Radiation
Monochromator Protocol
yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.18 10 91.7 0.099 0.099 -- 3.3 5840 5840 0.0 0.0 32.4
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)
2.18 2.26 67.6 0.246 0.246 3.2 2.0 438

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 2.18 10.0 0.0 0.0 5210 5210 561 91.65 0.27625 0.27625 0.27124 0.32364 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 2.181 2.254 390 41 349 0.318 0.388 -- 67.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 43.652
Anisotropic B[1][1] -3.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.28
Anisotropic B[2][2] -0.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.37
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.233
r_chiral_restr 0.095
r_mcangle_it 4.0
r_xyhbond_nbd_refined 0.236
r_mcbond_it 2.358
r_bond_refined_d 0.008
r_dihedral_angle_1_deg 3.628
r_scbond_it 2.117
r_gen_planes_refined 0.007
r_nbd_refined 0.266
r_angle_refined_deg 1.366
r_symmetry_hbond_refined 0.346
r_scangle_it 3.429
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 935
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 13

Software

Software
Software Name Purpose
R-AXIS data collection
d*TREK data reduction
AMoRE phasing
REFMAC refinement version: 5.1.19
R-AXIS data reduction
d*TREK data scaling