X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 298.0
Details 1.5M Ammonium Sulfate, 0.1 M Sodium Acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.54 α = 90
b = 99.32 β = 90
c = 144.84 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
CCD SBC-2 mirrors 2002-02-14
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9798 APS 19-ID

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 50 97.2 0.09 -- -- 8.1 97358 94632 2.0 2.0 36.0
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)
2.0 2.07 81.0 0.523 -- 1.87 4.9 9612

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
SAD 2.0 50.0 0.0 0.0 92365 89824 4738 97.25 -- 0.20163 0.19999 0.23262 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 2.0 2.047 -- 282 5243 0.24 0.279 -- 78.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.088
Anisotropic B[1][1] -0.63
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.59
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.751
r_dihedral_angle_3_deg 15.008
r_gen_planes_refined 0.004
r_chiral_restr 0.084
r_mcangle_it 1.411
r_symmetry_vdw_refined 0.198
r_nbtor_refined 0.3
r_bond_refined_d 0.01
r_angle_refined_deg 1.226
r_mcbond_it 0.803
r_dihedral_angle_2_deg 39.388
r_symmetry_hbond_refined 0.158
r_scbond_it 1.846
r_dihedral_angle_4_deg 16.9
r_xyhbond_nbd_refined 0.166
r_scangle_it 2.978
r_nbd_refined 0.199
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8566
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 542

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SBC-Collect data collection
HKL-2000 data scaling
CNS phasing