7K35

EQADH-NADH-4-METHYLBENZYL ALCOHOL, p21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VL0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS727810 MG/ML ENZYME DIALYZED AGAINST 50 MM AMMONIUM N-[TRIS(HYDROXYLMETHYL)METHYL]2-AMINOETHANE SULFONATE (PH 6.7 AT 25 DEG C) WITH 1 MM NAD+ AND 10 MM 4-METHY-BENZYL ALCOHOL AS THE CONCENTRATION OF 2-METHYL-2,4-PENTANEDIOL WAS RAISED TO 25 %. CRYSTAL WAS MOUNTED ON A FIBER LOOP AND FLASH VITRIFIED BY PLUNGING IT INTO LIQUID N2.
Crystal Properties
Matthews coefficientSolvent content
2.2545

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.22α = 90
b = 180.22β = 106.12
c = 86.86γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2006-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.9537APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.219.9699.20.1140.127.19.5345639015.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2498.20.5960.6437.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5vl01.219.96456320239999.1970.1770.17640.210223.888
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
3.3051.473-3.051-0.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.358
r_dihedral_angle_4_deg13.115
r_dihedral_angle_3_deg11.728
r_dihedral_angle_1_deg6.7
r_rigid_bond_restr4.132
r_scangle_it2.809
r_scangle_other2.809
r_scbond_it2.644
r_scbond_other2.644
r_lrange_it2.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.358
r_dihedral_angle_4_deg13.115
r_dihedral_angle_3_deg11.728
r_dihedral_angle_1_deg6.7
r_rigid_bond_restr4.132
r_scangle_it2.809
r_scangle_other2.809
r_scbond_it2.644
r_scbond_other2.644
r_lrange_it2.503
r_lrange_other2.409
r_angle_refined_deg2.134
r_mcangle_it1.677
r_mcangle_other1.677
r_mcbond_it1.588
r_mcbond_other1.585
r_angle_other_deg1.58
r_nbd_refined0.212
r_nbd_other0.187
r_symmetry_nbd_other0.184
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.145
r_symmetry_nbd_refined0.135
r_xyhbond_nbd_refined0.119
r_chiral_restr0.117
r_symmetry_nbtor_other0.086
r_symmetry_xyhbond_nbd_other0.042
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11140
Nucleic Acid Atoms
Solvent Atoms1248
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing