X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details PEG 400, MgCl2, HEPES.Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.21 α = 90
b = 89.86 β = 90
c = 264.58 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2004-09-24
CCD ADSC QUANTUM 4 mirrors 2004-07-07
Diffraction Radiation
Monochromator Protocol
si 111 MAD
si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 0.9801, 0.98033, 0.976071 SRS PX10.1
SYNCHROTRON SRS BEAMLINE PX14.2 0.978 SRS PX14.2

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
2.1 52.93 99.8 0.088 0.088 -- 4.3 -- 100581 -- -- 36.0
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)
2.24 2.36 99.6 0.35 0.35 3.4 3.1 14507

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 2.24 45.596 -- -- -- 100449 5084 99.673 0.188 0.188 0.1849 0.2385 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 2.24 2.298 -- 344 6885 0.328 0.424 -- 98.501
X Ray Diffraction 2.298 2.361 -- 347 6840 0.234 0.272 -- 99.819
X Ray Diffraction 2.361 2.429 -- 331 6607 0.224 0.253 -- 99.971
X Ray Diffraction 2.429 2.504 -- 333 6443 0.216 0.259 -- 100.0
X Ray Diffraction 2.504 2.585 -- 336 6219 0.205 0.252 -- 100.0
X Ray Diffraction 2.585 2.676 -- 360 5998 0.201 0.266 -- 100.0
X Ray Diffraction 2.676 2.777 -- 293 5864 0.199 0.28 -- 100.0
X Ray Diffraction 2.777 2.89 -- 323 5627 0.194 0.244 -- 100.0
X Ray Diffraction 2.89 3.017 -- 275 5427 0.198 0.262 -- 100.0
X Ray Diffraction 3.017 3.164 -- 251 5158 0.191 0.254 -- 100.0
X Ray Diffraction 3.164 3.334 -- 243 5001 0.186 0.242 -- 99.981
X Ray Diffraction 3.334 3.535 -- 244 4650 0.178 0.245 -- 100.0
X Ray Diffraction 3.535 3.778 -- 249 4424 0.172 0.255 -- 99.893
X Ray Diffraction 3.778 4.078 -- 245 4074 0.148 0.228 -- 99.884
X Ray Diffraction 4.078 4.464 -- 213 3785 0.142 0.178 -- 99.676
X Ray Diffraction 4.464 4.985 -- 199 3443 0.138 0.187 -- 99.535
X Ray Diffraction 4.985 5.745 -- 168 3036 0.169 0.18 -- 99.072
X Ray Diffraction 5.745 7.008 -- 154 2600 0.191 0.227 -- 98.674
X Ray Diffraction 7.008 9.796 -- 115 2061 0.149 0.171 -- 98.506
X Ray Diffraction 9.796 45.596 -- 61 1223 0.202 0.251 -- 95.252
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model anisotropic
Mean Isotropic B 31.21
Anisotropic B[1][1] 0.784
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.779
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.005
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 41.924
r_mcbond_it 0.593
r_chiral_restr 0.092
r_xyhbond_nbd_refined 0.205
r_angle_other_deg 0.88
r_nbd_other 0.195
r_scangle_other 0.997
r_mcangle_other 0.405
r_gen_planes_other 0.002
r_symmetry_vdw_refined 0.185
r_nbtor_other 0.096
r_scbond_other 0.658
r_symmetry_vdw_other 0.283
r_dihedral_angle_1_deg 5.936
r_mcangle_it 0.859
r_scangle_it 2.497
r_scbond_it 1.644
r_dihedral_angle_3_deg 16.908
r_bond_refined_d 0.016
r_mcbond_other 0.204
r_symmetry_hbond_refined 0.25
r_gen_planes_refined 0.005
r_dihedral_angle_4_deg 22.293
r_angle_refined_deg 1.484
r_bond_other_d 0.002
r_nbd_refined 0.208
r_nbtor_refined 0.183
r_xyhbond_nbd_other 0.151
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15898
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 806

Software

Software
Software Name Purpose
SCALA data scaling
SHELX phasing
RESOLVE phasing version: 2.08
REFMAC refinement version: refmac_5.2.0005
PDB_EXTRACT data extraction version: 1.700
MOSFLM data reduction
HKL-2000 data reduction
CCP4 data scaling version: (SCALA)
SCALEPACK data scaling
SHELXD phasing