X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.3
Temperature 289.0
Details 1.0 M Phosphate, 2.5% Benzamidine, 0.75 % Beta-octylglucoside, 25-250 mM NaCl equilibrated against 2.3 M Ammonium Sulphate at pH 9.5, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.05 α = 90
b = 117.05 β = 90
c = 298.44 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 VERTICALLY FOCUSING 1.2M Si MIRROR, MONOCHROMATED WITH A HORIZONTALLY FOCUSED Si(111) CRYSTAL 1997-06-25
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6

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 33 -- 0.051 -- -- 4.1 49320 48976 0.0 0.0 --
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)
2.0 2.05 95.0 0.306 -- 2.5 3.3 --

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
FOURIER SYNTHESIS 2.0 8.0 -- -- 52374 48976 2431 99.3 -- 0.1704 0.16943 0.19006 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 2.0 2.049 -- 170 3408 0.184 0.208 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Combined TLS and Isotropic refinement
Mean Isotropic B 22.962
Anisotropic B[1][1] 1.03
Anisotropic B[1][2] 0.51
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.54
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.107
r_nbd_other 0.269
r_nbd_refined 0.274
r_gen_planes_other 0.04
r_gen_planes_refined 0.019
r_chiral_restr 0.512
r_dihedral_angle_1_deg 6.484
r_angle_other_deg 1.508
r_angle_refined_deg 1.621
r_bond_other_d 0.014
r_bond_refined_d 0.019
r_xyhbond_nbd_refined 0.342
r_symmetry_vdw_refined 0.358
r_symmetry_vdw_other 0.369
r_symmetry_hbond_refined 0.408
r_mcbond_it 0.845
r_mcangle_it 1.487
r_scbond_it 1.941
r_scangle_it 2.61
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.109
Luzzati ESD (R-Free Set) 0.105
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2178
Nucleic Acid Atoms 0
Heterogen Atoms 1053
Solvent Atoms 230

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
DM Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
DM model building
SCALA data reduction
MOSFLM data collection