1VLL | pdb_00001vll

Crystal structure of alanine dehydrogenase (AF1665) from Archaeoglobus fulgidus at 2.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	0.05M Acetic Acid, 0.052M Citrate_Na3, 29% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		293	0.05M Acetic Acid, 0.05M Citrate_Na3, 30% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22
2.7	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.702	α = 90
b = 92.437	β = 90
c = 131.783	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC		2004-02-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC		2003-09-20	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794, 0.9796, 1.0000	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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
1,2	2.8	56.7	99.9	0.057	14.8	3.7		17713			84.89

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.8	2.87	99.8		0.362	2.3	3.3	1280

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.8	52.09	16757	897	99.79	0.21926	0.21742	0.22	0.2539	0.26	RANDOM	49.558

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]
-1.6			-1.47		3.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.526
r_dihedral_angle_3_deg	17.346
r_dihedral_angle_4_deg	16.672
r_scangle_it	6.284
r_dihedral_angle_1_deg	5.836
r_scbond_it	4.204
r_mcangle_it	2.049
r_angle_refined_deg	1.312
r_mcbond_it	1.184
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.526
r_dihedral_angle_3_deg	17.346
r_dihedral_angle_4_deg	16.672
r_scangle_it	6.284
r_dihedral_angle_1_deg	5.836
r_scbond_it	4.204
r_mcangle_it	2.049
r_angle_refined_deg	1.312
r_mcbond_it	1.184
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.24
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4574
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.