X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 10
Temperature 289.0
Details 4.06 M NaCl, 50 mM glycine, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 182.83 α = 90
b = 182.83 β = 90
c = 287.43 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-07-16
Diffraction Radiation
Monochromator Protocol
Si [1 1 1] MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 8-BM 0.9795, 0.9422, 0.9793 APS 8-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
3 129.1 99.97 0.081 -- -- 16.4 48895 48895 0.0 0.0 --
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)
3.0 3.15 100.0 0.16 -- 1.31 16.9 6574

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 3.0 29.75 -- 0.0 -- 48826 2458 100.0 0.257 -- 0.255 0.292 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 3.0 3.0771 -- 181 3335 0.283 0.331 -- --
X Ray Diffraction 3.077 3.1605 -- 174 3281 0.273 0.288 -- --
X Ray Diffraction 3.161 3.2511 -- 141 3194 0.304 0.331 -- --
X Ray Diffraction 3.251 3.3499 -- 167 3093 0.293 0.343 -- --
X Ray Diffraction 3.35 3.4583 -- 178 2990 0.296 0.326 -- --
X Ray Diffraction 3.458 3.5779 -- 177 2892 0.281 0.347 -- --
X Ray Diffraction 3.578 3.7109 -- 145 2812 0.292 0.336 -- --
X Ray Diffraction 3.711 3.8599 -- 124 2725 0.272 0.309 -- --
X Ray Diffraction 3.86 4.0285 -- 150 2620 0.262 0.312 -- --
X Ray Diffraction 4.028 4.2213 -- 122 2492 0.246 0.282 -- --
X Ray Diffraction 4.221 4.4446 -- 136 2369 0.233 0.29 -- --
X Ray Diffraction 4.445 4.7077 -- 122 2276 0.211 0.244 -- --
X Ray Diffraction 4.708 5.0237 -- 113 2125 0.222 0.251 -- --
X Ray Diffraction 5.024 5.4134 -- 104 2009 0.261 0.334 -- --
X Ray Diffraction 5.413 5.9105 -- 104 1851 0.286 0.329 -- --
X Ray Diffraction 5.911 6.5758 -- 100 1696 0.267 0.304 -- --
X Ray Diffraction 6.576 7.532 -- 70 1512 0.248 0.247 -- --
X Ray Diffraction 7.532 9.0804 -- 77 1302 0.204 0.261 -- --
X Ray Diffraction 9.08 12.2822 -- 42 1079 0.2 0.166 -- --
X Ray Diffraction 12.282 29.748 -- 31 715 0.345 0.365 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 40.457
Anisotropic B[1][1] 0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.169
r_mcbond_it 0.067
r_dihedral_angle_1_deg 4.658
r_chiral_restr 0.066
r_scangle_it 0.36
r_symmetry_hbond_refined 0.335
r_bond_refined_d 0.011
r_symmetry_vdw_refined 0.145
r_nbd_refined 0.151
r_angle_refined_deg 0.917
r_gen_planes_refined 0.004
r_scbond_it 0.233
r_mcangle_it 0.127
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11290
Nucleic Acid Atoms 0
Heterogen Atoms 208
Solvent Atoms 9

Software

Software
Software Name Purpose
SCALA data scaling version: CCP4_3.1.20
SHARP phasing
DM phasing version: 4.2
REFMAC refinement version: refmac_5.1.24
PDB_EXTRACT data extraction version: 1.502
MOSFLM data reduction
CCP4 data scaling version: (SCALA)