Experiment: 1M7J

Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	sodium citrate, ammonium acetate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.74	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.102	α = 90
b = 77.167	β = 90
c = 135.744	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 QUANTUM 4		2002-04-10	M	SINGLE WAVELENGTH
2	1	100	CCD	ADSC QUANTUM 4		2002-03-05

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-18B	0.9197	Photon Factory	BL-18B

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	1.5	50	99.2	0.047	50.5	6.3	101683	100783	1	1

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)
	1.5	1.55	100		0.116	17.6	6.6	9984

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.5	50	101683	100057	5056	98.4	0.161	0.161	0.16	0.164	0.174	random	10.8

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
c_angle_deg	1.77
c_bond_d	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3589
Nucleic Acid Atoms
Solvent Atoms	503
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
WARP	model building
HKL-2000	data reduction
CNS	phasing
ARP/wARP	model building