3BBF

Crystal structure of the NM23-H2 transcription factor complex with GDP

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	283	PEG 1500, 50 mM Tris-HCl, 200 mM MgCl2, 2 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.75	α = 90
b = 86.78	β = 90
c = 159.12	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	MAR CCD 165 mm	bent Si-mirror	2004-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.1271	APS	14-ID-B

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	1.7	30	96.6	0.062	25.4	6.5	103223	103223

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)
	1.7	1.76	81.4		0.33	3.3	4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1NUE	1.7	30	97878	5172	96.51	0.19811	0.19608	0.23592	RANDOM	15.833

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]
-0.26			0.01		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.997
r_dihedral_angle_4_deg	22.356
r_dihedral_angle_3_deg	14.619
r_dihedral_angle_1_deg	6.638
r_scangle_it	3.011
r_scbond_it	2.166
r_angle_refined_deg	1.669
r_mcangle_it	1.268
r_mcbond_it	1.068
r_angle_other_deg	1.029
r_symmetry_vdw_other	0.29
r_mcbond_other	0.245
r_nbd_refined	0.212
r_nbd_other	0.202
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_refined	0.12
r_chiral_restr	0.106
r_nbtor_other	0.085
r_metal_ion_refined	0.068
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7260
Nucleic Acid Atoms
Solvent Atoms	658
Heterogen Atoms	190

Software

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