X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 277.0
Details 2.0000M NaCl, 0.1M Acetate pH 4., NANODROP, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116 α = 90
b = 135.42 β = 90
c = 139.16 γ = 90
Symmetry
Space Group C 2 2 21

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) 2008-03-04
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 0.91837,0.97879,0.97932 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
2.4 29.84 98.7 0.078 0.078 -- 3.7 -- 42374 -- -- 54.294
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)
2.4 2.46 99.8 0.658 0.658 1.2 3.7 3119

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 2.4 29.841 -- 0.0 -- 42374 2140 98.3 -- 0.184 0.182 0.219 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 2.4 2.462 -- 156 2959 0.28 0.344 -- 99.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.537
Anisotropic B[1][1] 1.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.77
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.456
r_nbtor_other 0.084
r_mcbond_other 0.408
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_dihedral_angle_3_deg 14.934
r_symmetry_vdw_refined 0.233
r_bond_other_d 0.002
r_chiral_restr 0.081
r_metal_ion_refined 0.146
r_scangle_it 6.057
r_angle_other_deg 0.903
r_angle_refined_deg 1.37
r_symmetry_vdw_other 0.165
r_dihedral_angle_4_deg 14.456
r_nbd_other 0.193
r_bond_refined_d 0.017
r_symmetry_hbond_refined 0.033
r_dihedral_angle_2_deg 30.878
r_xyhbond_nbd_refined 0.224
r_dihedral_angle_1_deg 6.489
r_nbd_refined 0.196
r_mcbond_it 1.328
r_nbtor_refined 0.179
r_scbond_it 4.256
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4016
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 215

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