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_scangle_it 8.497
r_scbond_it 6.264
r_mcangle_it 3.161
r_mcbond_other 0.628
r_mcbond_it 2.511
r_symmetry_hbond_refined 0.111
r_symmetry_vdw_other 0.262
r_symmetry_vdw_refined 0.241
r_xyhbond_nbd_refined 0.228
r_nbtor_other 0.088
r_nbtor_refined 0.192
r_nbd_other 0.161
r_bond_refined_d 0.015
r_bond_other_d 0.001
r_angle_refined_deg 1.357
r_angle_other_deg 0.81
r_dihedral_angle_1_deg 5.647
r_dihedral_angle_2_deg 33.535
r_dihedral_angle_3_deg 15.877
r_dihedral_angle_4_deg 21.102
r_chiral_restr 0.08
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_nbd_refined 0.234
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

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.601 data extraction
SCALA data processing
REFMAC5 version: 5.2.0005 refinement