X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details 1.4M sodium acetate, 100mM sodium cacodylate, 5mM KCN, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.53 α = 90
b = 52.76 β = 87.75
c = 83.44 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2004-07-02
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 1.000 SPRING-8 BL45PX

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
1.68 50 99.9 -- 0.056 -- 4.9 39043 39043 0.0 0.0 14.64
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)
1.68 1.74 99.5 -- 0.286 4.03 4.1 3849

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 1.68 20.0 0.0 0.0 -- 37014 1927 99.8 -- 0.142 0.14 0.181 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 1.68 1.724 3849 135 2626 0.128 0.233 -- 97.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.13
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.3
Anisotropic B[2][2] -0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.46
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 2.638
r_sphericity_free 8.671
r_rigid_bond_restr 2.259
r_nbd_refined 0.229
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.108
r_dihedral_angle_4_deg 21.24
r_dihedral_angle_3_deg 13.768
r_dihedral_angle_2_deg 32.06
r_dihedral_angle_1_deg 4.677
r_angle_other_deg 0.89
r_angle_refined_deg 1.558
r_bond_other_d 0.001
r_bond_refined_d 0.018
r_nbd_other 0.179
r_nbtor_refined 0.189
r_nbtor_other 0.085
r_xyhbond_nbd_refined 0.182
r_symmetry_vdw_refined 0.253
r_symmetry_vdw_other 0.236
r_symmetry_hbond_refined 0.315
r_mcbond_it 1.973
r_mcbond_other 0.605
r_mcangle_it 2.215
r_scbond_it 3.516
r_scangle_it 4.751
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2710
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 265

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement