1HD7 | pdb_00001hd7

A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		TO BE PUBLISHED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.39	α = 90
b = 44.85	β = 124.54
c = 78.14	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC CCD	DUAL CRYSTAL MIRROR	1999-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5		SSRL	BL1-5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.95	25	99.4	0.082	6.6	3.3		34905			29.68

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	1.95	2.01	99.2		0.47	1.5	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	TO BE PUBLISHED	1.95	25	26771	2699	92.2	0.205	0.2	0.255	RANDOM	37.4

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
p_transverse_tor	31.7
p_staggered_tor	18.1
p_planar_tor	8.4
p_scangle_it	3.4
p_mcangle_it	2.7
p_scbond_it	2.2
p_mcbond_it	1.8
p_multtor_nbd	0.261
p_singtor_nbd	0.185
p_chiral_restr	0.15
p_xyhbond_nbd	0.125
p_planar_d	0.069
p_angle_d	0.038
p_plane_restr	0.03
p_bond_d	0.016
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2070
Nucleic Acid Atoms
Solvent Atoms	288
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
EPMR	phasing