X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 298.0
Details 52% MPD, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.02 α = 90
b = 84.43 β = 98.81
c = 45.99 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 MARRESEARCH -- 2001-04-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.97 SSRL BL9-1

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
1.03 47.46 97.4 0.037 -- -- -- 206004 206004 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)
1.03 1.05 99.8 0.222 -- -- -- 10544

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
Isomorphous to previous structure 1.03 47.46 -- 0.0 209009 198537 10472 95.46 0.1178 0.1178 0.1169 0.135 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 1.03 1.057 -- 793 15052 0.144 0.164 -- 99.87
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.428
Anisotropic B[1][1] -0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.04
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 28.321
r_scbond_it 3.784
r_scangle_it 5.002
r_dihedral_angle_3_deg 12.003
r_mcangle_it 3.662
r_bond_other_d 0.002
r_gen_planes_other 0.004
r_mcbond_it 2.648
r_bond_refined_d 0.016
r_gen_planes_refined 0.01
r_mcbond_other 2.701
r_sphericity_bonded 5.662
r_chiral_restr 0.281
r_angle_other_deg 1.257
r_sphericity_free 10.035
r_dihedral_angle_1_deg 7.654
r_dihedral_angle_4_deg 15.078
r_angle_refined_deg 1.818
r_rigid_bond_restr 1.967
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3625
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 576

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
Blu-Ice data collection
Fc phasing version: calculation