X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.9
Temperature 277.0
Details 0.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.56 α = 90
b = 55.18 β = 94.31
c = 47.12 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2008-04-11
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 -- 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
1.7 28.68 99.6 0.098 0.098 -- 7.4 -- 25116 -- -- 24.306
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)
1.7 1.74 95.7 0.871 0.871 0.9 7.0 1763

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
SAD 1.7 28.677 -- 0.0 -- 25099 1283 99.63 -- 0.176 0.174 0.22 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 1.7 1.744 -- 74 1685 0.27 0.365 -- 95.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.342
Anisotropic B[1][1] 0.37
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.05
Anisotropic B[2][2] 0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_nbtor_refined 0.175
r_xyhbond_nbd_refined 0.116
r_nbtor_other 0.089
r_dihedral_angle_3_deg 12.758
r_bond_other_d 0.001
r_scbond_it 4.374
r_nbd_other 0.21
r_symmetry_hbond_refined 0.171
r_gen_planes_refined 0.006
r_chiral_restr 0.087
r_scangle_it 5.982
r_dihedral_angle_1_deg 6.224
r_mcbond_it 1.914
r_symmetry_vdw_refined 0.134
r_angle_refined_deg 1.494
r_mcangle_it 2.717
r_bond_refined_d 0.015
r_dihedral_angle_2_deg 41.188
r_nbd_refined 0.193
r_angle_other_deg 0.845
r_dihedral_angle_4_deg 16.805
r_symmetry_vdw_other 0.18
r_mcbond_other 0.552
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1439
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 283

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SOLVE phasing
MolProbity model building version: 3beta29
SCALA data scaling
PDB_EXTRACT data extraction version: 3.004
MOSFLM data reduction