X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 291.0
Details ammonium sulfate, glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.41 α = 90
b = 116.36 β = 90
c = 40.17 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 -- 2003-03-23
Diffraction Radiation
Monochromator Protocol
Channel-cut Si crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.9792, 0.9795, 0.9611 NSLS X12C

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 30 98.4 0.061 -- -- 13.7 20786 20786 0.0 0.0 34.7
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 94.5 0.51 -- 3.7 10.3 --

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
MAD 2.0 29.3 -- 0.0 19686 19686 1061 98.33 0.2102 0.20468 0.20291 0.23718 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 2.053 1414 77 1337 0.277 0.38 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.416
Anisotropic B[1][1] 0.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.53
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.229
r_symmetry_hbond_refined 0.156
r_bond_refined_d 0.017
r_symmetry_vdw_refined 0.177
r_scbond_it 3.809
r_angle_refined_deg 1.358
r_gen_planes_refined 0.006
r_scangle_it 6.523
r_chiral_restr 0.095
r_mcbond_it 1.304
r_dihedral_angle_1_deg 4.055
r_xyhbond_nbd_refined 0.2
r_mcangle_it 2.518
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2036
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 225

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
CBASS data collection
SCALEPACK data scaling
SOLVE phasing