3U8U | pdb_00003u8u

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HD7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	280	0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.84	α = 90
b = 97.284	β = 90.91
c = 132.15	γ = 90

Symmetry
Space Group	P 1 21 1

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 315	mirrors	2007-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.1	NSLS	X12C

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	2.15	50	99.4	0.05	15.1	7.1	131267	131267

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	2.15	2.23	97.4		0.28	3.5	5.5	12822

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1HD7	2.15	40.71	131267	124519	6601	99.27	0.19995	0.19768	0.1972	0.24337	0.2411	RANDOM	31.823

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]
		0.01	-0.02		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.446
r_dihedral_angle_4_deg	18.631
r_dihedral_angle_3_deg	17.929
r_dihedral_angle_1_deg	8.451
r_scangle_it	5.442
r_scbond_it	3.804
r_mcangle_it	2.363
r_mcbond_it	1.391
r_angle_refined_deg	1.186
r_chiral_restr	0.083
r_gen_planes_refined	0.015
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12786
Nucleic Acid Atoms
Solvent Atoms	835
Heterogen Atoms	10

Software

Software
Software Name	Purpose
CBASS	data collection
MOLREP	phasing
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling