X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 277.0
Details 2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 31.91 α = 90
b = 46.25 β = 90
c = 52.65 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 MAR CCD 165 mm MIRRORS 2002-03-04
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6

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
1.5 34.75 96.5 0.078 -- -- 2.5 12884 12433 -- 2.0 13.11
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)
1.5 1.53 95.1 0.465 -- 2.1 2.4 634

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 1.5 34.75 -- -- 12425 11814 602 95.08 -- 0.15325 0.15002 0.21657 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 1.5 1.537 656 37 656 0.224 0.36 -- 74.44
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 14.47
Anisotropic B[1][1] -0.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.32
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.184
r_gen_planes_refined 0.013
r_symmetry_vdw_refined 0.225
r_angle_refined_deg 2.423
r_nbd_refined 0.232
r_scbond_it 3.766
r_symmetry_hbond_refined 0.235
r_nbtor_refined 0.314
r_dihedral_angle_3_deg 13.047
r_xyhbond_nbd_refined 0.229
r_bond_refined_d 0.029
r_scangle_it 5.566
r_dihedral_angle_1_deg 6.95
r_dihedral_angle_2_deg 34.347
r_mcbond_it 1.673
r_mcangle_it 2.257
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 737
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 118

Software

Software
Software Name Purpose
MAR345 data collection
MOLREP phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling