X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 20% PEG 10000, 0.1M HEPES, 0.3M glycyl-glycyl-glycine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.4 α = 90
b = 83.82 β = 92.1
c = 75.24 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 MAR CCD 225 mm -- 2006-06-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.97969 APS 22-BM

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
1.9 50.48 98.0 0.04 -- -- -- -- 49897 -- -- --
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)
1.9 1.97 91.3 -- 0.17 7.1 -- --

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 1.9 30.0 -- 0.0 -- 48766 2475 97.76 -- 0.209 0.207 0.25 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 1.905 1.955 3182 172 3010 0.228 0.298 -- 87.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.319
Anisotropic B[1][1] 0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.98
Anisotropic B[2][2] 0.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.78
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.017
r_symmetry_hbond_refined 0.206
r_chiral_restr 0.116
r_symmetry_vdw_refined 0.27
r_angle_refined_deg 1.637
r_dihedral_angle_3_deg 15.198
r_dihedral_angle_2_deg 33.64
r_scbond_it 3.104
r_dihedral_angle_1_deg 6.104
r_mcbond_it 1.491
r_nbd_refined 0.217
r_dihedral_angle_4_deg 18.19
r_nbtor_refined 0.309
r_mcangle_it 1.813
r_metal_ion_refined 0.042
r_xyhbond_nbd_refined 0.145
r_gen_planes_refined 0.007
r_scangle_it 4.618
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3873
Nucleic Acid Atoms 0
Heterogen Atoms 113
Solvent Atoms 259

Software

Software
Software Name Purpose
REFMAC refinement
PDB_EXTRACT data extraction version: 2.000
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing