X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 6.2
Temperature 277.0
Details 35.0% 2-ethoxyethanol, 0.2M NaCl, 0.1M Na,K-Phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.56 α = 90
b = 135.56 β = 90
c = 35.56 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Flat mirror (vertical focusing) 2005-12-18
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.979224, 0.918370, 0.978940 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 27.9 94.7 0.041 -- -- -- -- 22105 -- -- 42.314
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)
2.0 2.07 83.8 0.415 -- 2.0 -- --

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 2.0 27.94 -- 0.0 -- 22103 1130 99.26 -- 0.223 0.22 0.278 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 2.001 2.053 1599 95 1504 0.257 0.306 -- 99.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.573
Anisotropic B[1][1] -0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.91
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_scangle_it 6.14
r_bond_other_d 0.003
r_bond_refined_d 0.013
r_angle_other_deg 1.188
r_symmetry_vdw_refined 0.145
r_mcangle_it 2.42
r_scbond_it 4.208
r_mcbond_it 1.427
r_nbd_other 0.123
r_chiral_restr 0.107
r_symmetry_vdw_other 0.109
r_symmetry_hbond_refined 0.22
r_angle_refined_deg 1.684
r_nbtor_refined 0.165
r_dihedral_angle_2_deg 25.182
r_nbd_refined 0.18
r_nbtor_other 0.081
r_mcbond_other 0.385
r_xyhbond_nbd_refined 0.169
r_gen_planes_other 0.002
r_dihedral_angle_4_deg 8.252
r_dihedral_angle_1_deg 2.099
r_dihedral_angle_3_deg 8.319
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2346
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 107

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
XSCALE data scaling
PDB_EXTRACT data extraction version: 1.701
XDS data reduction
SHARP phasing version: V. 1