1L6G

Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L6F	PDB 1L6F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.787	α = 90
b = 90.714	β = 90
c = 85.27	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	293	AREA DETECTOR	SIEMENS HI-STAR	carbon monochrometer	1998-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	MACSCIENCE	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1	1.94	38.76	86.87	0.077	6.67	4	50473	50473			7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.939	2.009	76.1		0.496	1.64	1.81	5583

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB 1L6F	2	7.99	2	39514	3982	75.9	0.169	0.169	0.216	RANDOM	22.7

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]
-0.08			2.57		-2.49

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.6
c_scangle_it	4.78
c_scbond_it	3.46
c_mcangle_it	2.9
c_mcbond_it	2
c_angle_deg	1.3
c_improper_angle_d	0.69
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6066
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	42

Software

Software
Software Name	Purpose
SAINT	data scaling
SAINT	data reduction
X-PLOR	model building
CNS	refinement
X-PLOR	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.