1I8M | pdb_00001i8m

CRYSTAL STRUCTURE OF A RECOMBINANT ANTI-SINGLE-STRANDED DNA ANTIBODY FRAGMENT COMPLEXED WITH DT5

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	2 M ammonium sulfate, 0.1 M sodium acetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.1	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 171.84	α = 90
b = 171.84	β = 90
c = 144.568	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	173	CCD	ADSC QUANTUM 4		1999-09-21	M	SINGLE WAVELENGTH
2	1	x-ray	173	CCD	ADSC QUANTUM 4		2000-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.979	NSLS	X8C
2	SYNCHROTRON	NSLS BEAMLINE X12B	0.978	NSLS	X12B

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	2.1	28	99	0.079	19.3	6.8	72520	72520			23

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)
	2.1	2.18	96		0.294	3.6	3.6

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 (All)	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	1mlc	2.1	27.66	72520	72520	7190	98.8	0.229	0.2203	0.2203	0.23	0.2583	0.26	RANDOM	38.5

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]
3.79	1.06		3.79		-7.57

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	27.37438
c_scangle_it	2.93
c_scbond_it	2.09
c_mcangle_it	2.05
c_angle_deg	1.62386
c_mcbond_it	1.33
c_improper_angle_d	0.99896
c_bond_d	0.011155

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6414
Nucleic Acid Atoms	121
Solvent Atoms	339
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	model building
CNS	refinement
X-PLOR	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.