X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 0.85M Sodium Citrate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.32 α = 90
b = 75.37 β = 90
c = 87.78 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV AXCO 2006-07-06
Diffraction Radiation
Monochromator Protocol
Ni Filter 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
2.2 50 97.9 0.106 -- -- 3.5 -- 22532 -- -- --
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)
2.2 2.28 100.0 0.397 -- 4.2 3.5 2262

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 2.2 21.94 -- -- -- 21328 1152 97.73 -- 0.20128 0.19872 0.24931 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 2.199 2.256 -- 83 1551 0.299 0.367 -- 97.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.433
Anisotropic B[1][1] -1.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.2
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.134
r_scbond_it 1.694
r_nbd_other 0.182
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.174
r_scangle_it 2.528
r_dihedral_angle_2_deg 35.762
r_nbtor_refined 0.198
r_dihedral_angle_3_deg 17.329
r_symmetry_vdw_other 0.261
r_xyhbond_nbd_refined 0.19
r_angle_other_deg 0.847
r_bond_refined_d 0.014
r_nbtor_other 0.092
r_dihedral_angle_4_deg 22.102
r_chiral_restr 0.079
r_angle_refined_deg 1.505
r_bond_other_d 0.001
r_mcbond_it 0.936
r_dihedral_angle_1_deg 5.772
r_mcbond_other 0.153
r_nbd_refined 0.215
r_mcangle_it 1.136
r_gen_planes_other 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2267
Nucleic Acid Atoms 0
Heterogen Atoms 119
Solvent Atoms 201

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
CrystalClear data collection
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing