2PG4 | pdb_00002pg4

Crystal structure of a putative dna binding protein (ape_0880a) from aeropyrum pernix k1 at 2.21 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	NANODROP, 1.0M LiCl, 10.0% PEG 6000, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.84	α = 90
b = 109.84	β = 90
c = 36.76	γ = 90

Symmetry
Space Group	P 4 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	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-02-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97929	SSRL	BL9-2

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	2.21	29.437	95.4	0.062	11.29			11747			52.45

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	2.21	2.27	63.1		0.464	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	2.21	29.43	11725	563	98.87	0.20083	0.19797	0.2	0.25754	0.27	RANDOM	40.916

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]
-0.23			-0.23		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.916
r_dihedral_angle_4_deg	21.021
r_dihedral_angle_3_deg	17.542
r_scangle_it	7.142
r_dihedral_angle_1_deg	6.11
r_scbond_it	5.915
r_mcangle_it	3.117
r_mcbond_it	2.133
r_angle_refined_deg	1.65
r_angle_other_deg	0.936
r_mcbond_other	0.53
r_symmetry_vdw_other	0.229
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.204
r_symmetry_vdw_refined	0.195
r_nbd_other	0.181
r_nbtor_refined	0.177
r_nbtor_other	0.086
r_chiral_restr	0.075
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1453
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	51

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing