1ZS7

The structure of gene product APE0525 from Aeropyrum pernix

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	293	K/Na Phosphate, glycerol, ethylene glycol, sucrose, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.85	α = 90
b = 112.792	β = 90
c = 39.001	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	CUSTOM-MADE		2004-12-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97940, 0.97959	APS	19-BM

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	1.85	36.9	94.4	0.079	17.2	4.5	19171	19171

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92	79.9		0.434	2.1	2.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.85	36.86	18045	17112	933	94.44	0.1683	0.1683	0.16668	0.19883	RANDOM	19.906

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]
0.45			-0.15		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.94
r_dihedral_angle_4_deg	15.492
r_dihedral_angle_3_deg	12.873
r_dihedral_angle_1_deg	5.553
r_scangle_it	3.865
r_scbond_it	2.35
r_angle_refined_deg	1.287
r_mcangle_it	1.24
r_mcbond_it	0.644
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.209
r_metal_ion_refined	0.181
r_symmetry_metal_ion_refined	0.181
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1470
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing
ARP/wARP	model building