3BBB | pdb_00003bbb

Crystal structure of the NM23-H2 transcription factor complex with dinucleotide d(AG)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NUE	pdb entry 1NUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG 1500, 50 mM sodium citrate, 20 mM MgCl2, 5 mM DTT, Crystals soaked with 10 mM d(AG), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.466	α = 90
b = 118.219	β = 90
c = 128.91	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2003-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9000	APS	14-BM-C

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	1.3	27	99.3	0.086	16.4	8		195789

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	1.3	1.35	98.3		0.42	2.3	6.8

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-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 1NUE	1.3	27	183782	9678	98.2	0.177	0.175	0.18	0.22	0.23	RANDOM	14.16

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]
0.11			0.21		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.612
r_dihedral_angle_4_deg	21.777
r_dihedral_angle_3_deg	13.714
r_sphericity_free	10.771
r_dihedral_angle_1_deg	6.384
r_sphericity_bonded	5.741
r_scangle_it	4.791
r_scbond_it	3.688
r_mcangle_it	2.699
r_rigid_bond_restr	2.399
r_mcbond_it	2.265
r_angle_refined_deg	1.885
r_mcbond_other	1.237
r_angle_other_deg	1.202
r_nbd_refined	0.227
r_nbd_other	0.215
r_symmetry_vdw_other	0.21
r_chiral_restr	0.187
r_nbtor_refined	0.187
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.137
r_nbtor_other	0.084
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7218
Nucleic Acid Atoms
Solvent Atoms	641
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data collection
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing