1KT9

Crystal Structure of C. elegans Ap4A Hydrolase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.794	α = 90
b = 72.934	β = 90
c = 61.046	γ = 90

Symmetry
Space Group	C 2 2 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		2000-07-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87	SRS	PX9.6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.98	18	99.8			53439	9864	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.98	2.05	97.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.98	20	9389	9389	474	98	0.19715	0.19631	0.2132	RANDOM	14.727

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]
0.59			0.98		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.81
r_dihedral_angle_1_deg	5.248
r_scangle_it	3.416
r_scbond_it	2.248
r_angle_refined_deg	1.627
r_mcangle_it	1.528
r_mcbond_it	0.893
r_angle_other_deg	0.812
r_symmetry_vdw_other	0.432
r_symmetry_vdw_refined	0.343
r_nbd_refined	0.247
r_nbd_other	0.217
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_nbtor_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1032
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms

Software

Software
Software Name	Purpose
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling