4KZF | pdb_00004kzf

The mechanism of the amidases: The effect of the mutation E142L in the amidase from Geobacillus pallidus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PLQ	PDB entry 2PLQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	294	1.2M sodium citrate, 0.4M sodium chloride, 0.1M sodium acetate, pH 5.6, vapor diffusion, hanging drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.979	α = 90
b = 130.979	β = 90
c = 130.979	γ = 90

Symmetry
Space Group	P 42 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	100	CCD			2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.8856	ESRF	BM14

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	1.84	92.62	99.7	0.08	10.6	6.58	33703	33703	3	3	29.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2PLQ	1.85	36.3	33255	33155	1690	99.34	0.1861	0.1861	0.1852	0.19	0.2028	0.21	RANDOM	23.3198

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.255
r_dihedral_angle_4_deg	19.556
r_dihedral_angle_3_deg	12.042
r_dihedral_angle_1_deg	7.105
r_angle_refined_deg	1.941
r_angle_other_deg	0.959
r_chiral_restr	0.141
r_bond_refined_d	0.024
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.255
r_dihedral_angle_4_deg	19.556
r_dihedral_angle_3_deg	12.042
r_dihedral_angle_1_deg	7.105
r_angle_refined_deg	1.941
r_angle_other_deg	0.959
r_chiral_restr	0.141
r_bond_refined_d	0.024
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2640
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	1

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
d*TREK	data reduction
d*TREK	data scaling
REFMAC	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.