X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 4.5
Temperature 293.0
Details 30.0% PEG-8000, 0.2M MgNO3, 0.1M Citrate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.52 α = 90
b = 87.11 β = 110.73
c = 59.16 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 Flat mirror 2005-04-03
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.918370, 0.979508 SSRL BL11-1

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
2.3 29.18 99.5 -- 0.093 -- 5.0 -- 21323 -- -- --
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)
2.3 2.36 95.8 -- 0.612 1.2 3.7 --

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 2.3 29.18 -- -- -- 20200 1105 99.77 0.204 0.20399 0.201 0.264 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 2.301 2.36 -- 85 1470 0.237 0.305 -- 99.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.288
Anisotropic B[1][1] -2.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.25
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.15
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_mcbond_it 2.511
r_angle_other_deg 0.81
r_gen_planes_other 0.001
r_nbtor_refined 0.192
r_mcbond_other 0.628
r_symmetry_hbond_refined 0.111
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 5.647
r_mcangle_it 3.161
r_nbtor_other 0.088
r_scangle_it 8.497
r_chiral_restr 0.08
r_nbd_refined 0.234
r_nbd_other 0.161
r_dihedral_angle_2_deg 33.535
r_symmetry_vdw_refined 0.241
r_symmetry_vdw_other 0.262
r_dihedral_angle_4_deg 21.102
r_xyhbond_nbd_refined 0.228
r_bond_refined_d 0.015
r_dihedral_angle_3_deg 15.877
r_scbond_it 6.264
r_angle_refined_deg 1.357
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3268
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 56

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
SCALA data scaling
PDB_EXTRACT data extraction version: 1.601
MOSFLM data reduction
CCP4 data scaling version: (SCALA)
SOLVE phasing