X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 291.0
Details 20% PEG3350, 0.2 Sodium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.97 α = 90
b = 88.64 β = 90.01
c = 57.88 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
CCD ADSC QUANTUM 4 -- 2005-05-26
Diffraction Radiation
Monochromator Protocol
Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.0 SPRING-8 BL12B2

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
2.07 30 97.4 0.046 -- -- -- -- 34426 -- -- --
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)
2.07 2.14 97.4 -- -- -- -- --

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 2.07 30.0 -- -- -- 31791 1687 97.16 -- 0.22228 0.21859 0.28835 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 2.07 2.124 -- 135 2258 0.217 0.318 -- 96.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.691
Anisotropic B[1][1] 1.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.65
Anisotropic B[2][2] -0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.19
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.096
r_scbond_it 3.83
r_mcbond_it 1.967
r_nbd_refined 0.241
r_gen_planes_refined 0.01
r_chiral_restr 0.149
r_dihedral_angle_4_deg 18.918
r_dihedral_angle_3_deg 18.428
r_dihedral_angle_2_deg 39.615
r_dihedral_angle_1_deg 7.022
r_angle_refined_deg 1.919
r_bond_refined_d 0.021
r_nbtor_refined 0.314
r_xyhbond_nbd_refined 0.194
r_symmetry_vdw_refined 0.348
r_symmetry_hbond_refined 0.194
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4356
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 140

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
MOLREP model building
SCALEPACK data reduction
HKL-2000 data collection