1SK8 | pdb_00001sk8

Crystallographic snapshots of Aspergillus fumigatus phytase revealing its enzymatic dynamics

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	300	PEG 4000, magnesium chloride hexahydrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.714	α = 90
b = 99.484	β = 90
c = 100.751	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 210	mirrors	2003-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		CHESS	A1

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	1.65	30	93.5			48970	45787	2	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	1.65	1.68	80.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.65	30	2	48970	45787	2708	93.5	0.17765	0.1748	0.1984	0.23061	RANDOM	25.131

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]
-1.24			2.72		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.206
r_scangle_it	5.376
r_scbond_it	3.837
r_mcangle_it	2.368
r_angle_refined_deg	1.571
r_mcbond_it	1.527
r_symmetry_vdw_refined	0.4
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.206
r_scangle_it	5.376
r_scbond_it	3.837
r_mcangle_it	2.368
r_angle_refined_deg	1.571
r_mcbond_it	1.527
r_symmetry_vdw_refined	0.4
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3374
Nucleic Acid Atoms
Solvent Atoms	397
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.