1XF4 | pdb_00001xf4

Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I8M	PDB ENTRY 1I8M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.9	298	ammonium sulfate, sodium acetate, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.4	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.179	α = 90
b = 179.179	β = 90
c = 91.985	γ = 120

Symmetry
Space Group	P 3 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	173	CCD	ADSC QUANTUM 4		2001-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.072	NSLS	X8C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	49.5	87	0.09	0.09	13	5.8	54454	54454

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	81		0.511	0.511	2.9

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	PDB ENTRY 1I8M	2.5	49.5	51454	41498	4384	77.8	0.18696	0.18696	0.18303	0.18	0.22398	0.22	RANDOM	23.847

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]
-0.29	-0.15		-0.29		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.066
r_scangle_it	2.315
r_scbond_it	1.512
r_angle_refined_deg	1.511
r_mcangle_it	0.973
r_mcbond_it	0.53
r_symmetry_vdw_refined	0.265
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6360
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing