5FJU | pdb_00005fju

N-acyl amino acid racemase from Amycolatopsis sp. Ts-1-60: Q26A M50I G291D F323Y mutant in complex with N-acetyl phenylalanine

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4A6G	PDB ENTRY 4A6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		100 MM TRIS HCL PH 8.0; 15% (W/V) PEG 4K; 800 MM SODIUM FORMATE; PROTEIN AT 8 MG PER ML

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.9	α = 90
b = 216.9	β = 90
c = 261.63	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	PIXEL	DECTRIS PILATUS 6M		2014-12-07	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	2.52	107.35	100	0.1	17	10.2		79550		2

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	2.52	2.59	100		0.83	2.9	10

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 4A6G	2.52	107.35	75765	3783	99.98	0.158	0.15635	0.16	0.1902	0.2	RANDOM	47.372

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]
-1.04	-0.52		-1.04		3.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.375
r_dihedral_angle_4_deg	21.936
r_dihedral_angle_3_deg	16.223
r_dihedral_angle_1_deg	6.025
r_scbond_it	5.326
r_mcangle_it	5.26
r_mcbond_it	3.785
r_mcbond_other	3.781
r_angle_refined_deg	1.809
r_angle_other_deg	1.488
r_chiral_restr	0.102
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.009
r_gen_planes_other	0.008
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_mcangle_other
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	10968
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing