X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details 0.1M HEPES PH 6.5, 6% PEG 8000 (W/V), 5MM NISO4, 50 MM NITROBENZENE. THE NITROBENZENE WAS PREPARED FROM A 1M STOCKSOLUTION WHERE NITROBENZENE WAS DISOLVED IN ETHANOL.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 121.53 α = 90
b = 121.53 β = 90
c = 84.18 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2003-11-22
Diffraction Radiation
Monochromator Protocol
SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 -- MAX II I711

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
1.55 27.63 98.5 0.08 -- -- 5.1 -- 99964 -- 1.0 --
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)
1.55 1.63 99.7 0.51 -- 1.4 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 1.55 27.0 -- -- -- 95726 5050 98.5 -- 0.169 0.167 0.192 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 1.55 1.59 -- 348 7146 0.244 0.27 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.71
Anisotropic B[1][1] -0.44
Anisotropic B[1][2] -0.22
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.44
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.65
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.132
r_mcangle_it 1.095
r_bond_refined_d 0.01
r_dihedral_angle_1_deg 6.234
r_scangle_it 2.55
r_angle_refined_deg 1.306
r_dihedral_angle_4_deg 17.613
r_nbtor_refined 0.308
r_nbd_refined 0.199
r_symmetry_vdw_refined 0.227
r_dihedral_angle_2_deg 35.413
r_dihedral_angle_3_deg 12.073
r_xyhbond_nbd_refined 0.11
r_scbond_it 1.779
r_chiral_restr 0.092
r_gen_planes_refined 0.005
r_mcbond_it 0.658
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5048
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 699

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
MOSFLM data reduction
SCALA data scaling