X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.6
Temperature 298.0
Details PEG 4000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.2 α = 90
b = 42.1 β = 95.88
c = 65.85 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 osmic mirrors 2002-07-08
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 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
1.8 21 98.5 -- 0.064 -- 3.6 25024 24988 0.0 0.0 19.9
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 1.85 96.5 -- 0.31 2.4 3.6 1859

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 21.0 0.0 0.0 23852 23852 1214 99.66 0.1532 0.15323 0.151 0.19788 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 1780 79 1780 0.284 0.356 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 22.693
Anisotropic B[1][1] -0.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.94
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.24
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.703
r_scbond_it 3.585
r_mcangle_it 2.528
r_mcbond_it 1.366
r_symmetry_hbond_refined 0.376
r_symmetry_vdw_other 0.212
r_symmetry_vdw_refined 0.171
r_bond_refined_d 0.024
r_bond_other_d 0.002
r_angle_refined_deg 1.968
r_angle_other_deg 0.945
r_dihedral_angle_1_deg 6.88
r_chiral_restr 0.122
r_gen_planes_refined 0.011
r_gen_planes_other 0.009
r_nbd_refined 0.204
r_nbd_other 0.247
r_nbtor_other 0.09
r_xyhbond_nbd_refined 0.159
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.11
Luzzati ESD (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2227
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 163

Software

Computing
Computing Package Purpose
CRYSTALCLEAR (MSC/RIGAKU) Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
MLPHARE Structure Solution
REFMAC 5.1.22 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.22 refinement