7K35 | pdb_00007k35

EQADH-NADH-4-METHYLBENZYL ALCOHOL, p21

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VL0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	10 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 coefficient	Solvent content
2.25	45

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2006-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9537	APS	23-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.2	19.96	99.2	0.114	0.12	7.1	9.53		456390			15.8

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)	Redundancy	Number Unique Reflections (All)
1	1.2	1.24	98.2		0.596	0.643	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5vl0	1.2	19.96	456320	2399	99.197	0.177	0.1764	0.18	0.2102	0.21	23.888

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]
3.305		1.473	-3.051		-0.947

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.358
r_dihedral_angle_4_deg	13.115
r_dihedral_angle_3_deg	11.728
r_dihedral_angle_1_deg	6.7
r_rigid_bond_restr	4.132
r_scangle_it	2.809
r_scangle_other	2.809
r_scbond_it	2.644
r_scbond_other	2.644
r_lrange_it	2.503
r_lrange_other	2.409
r_angle_refined_deg	2.134
r_mcangle_it	1.677
r_mcangle_other	1.677
r_mcbond_it	1.588
r_mcbond_other	1.585
r_angle_other_deg	1.58
r_nbd_refined	0.212
r_nbd_other	0.187
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbd_refined	0.135
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.117
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_other	0.042
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11140
Nucleic Acid Atoms
Solvent Atoms	1248
Heterogen Atoms	236

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
REFMAC	phasing