X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 298.0
Details PEG 4000, sodium acetate, Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 28.97 α = 90
b = 31.28 β = 97.09
c = 29.78 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 315 -- 2004-11-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.009 NSLS X29A

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
1.6 50 97.5 0.037 -- -- -- -- 6979 -- -- 14.0
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)
1.6 1.66 94.5 0.168 -- 10.5 -- --

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 1.6 29.49 -- -- -- 6604 323 97.45 -- 0.14457 0.1424 0.18774 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 1.6 1.642 -- 30 476 0.167 0.169 -- 95.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.417
Anisotropic B[1][1] 2.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.67
Anisotropic B[2][2] -1.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.94
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.677
r_mcbond_it 1.28
r_dihedral_angle_3_deg 10.804
r_nbtor_refined 0.32
r_scangle_it 4.52
r_mcangle_it 1.91
r_chiral_restr 0.137
r_nbd_refined 0.214
r_xyhbond_nbd_refined 0.177
r_dihedral_angle_4_deg 7.993
r_gen_planes_refined 0.009
r_symmetry_vdw_refined 0.172
r_dihedral_angle_1_deg 6.864
r_scbond_it 3.116
r_symmetry_hbond_refined 0.179
r_bond_refined_d 0.017
r_dihedral_angle_2_deg 39.599
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 512
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 120

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0003
HKL-2000 data reduction
SCALEPACK data scaling
PHASES phasing