4A6G | pdb_00004a6g

N-acyl amino acid racemase from Amycalotopsis sp. Ts-1-60: G291D- F323Y mutant in complex with N-acetyl methionine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		PROTEIN CONCENTRATION OF 8 MG ML-1 THAT HAD BEEN INCUBATED PREVIOUSLY WITH 10 MM N-ACETYL METHIONINE. CRYSTAL DROPS CONTAINED 100 MM TRIS-HCL (PH 8.0) 15% PEG 4K, 800 MM NA FORMATE

Crystal Properties
Matthews coefficient	Solvent content
3.74	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.71	α = 90
b = 216.71	β = 90
c = 261.1	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC CCD		2011-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	2.71	88.31	100	0.08	18.6	10.2		60693		4.8

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	2.71	2.79	100		0.5	4.8	10.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SJA	2.71	88.31	60693	3226	99.97	0.15816	0.15535	0.15	0.21012	0.21	RANDOM	47.754

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]
-0.2	-0.1		-0.2		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.304
r_dihedral_angle_4_deg	23.185
r_dihedral_angle_3_deg	20.631
r_dihedral_angle_1_deg	6.891
r_angle_refined_deg	2.097
r_chiral_restr	0.138
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10897
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing