4KG0 | pdb_00004kg0

Crystal structure of the drosophila melanogaster neuralized-nhr1 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YUE	PDB ENTRY 2YUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.4M MAGNESIUM NITRATE, 10% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.28	α = 90
b = 89.28	β = 90
c = 36.93	γ = 120

Symmetry
Space Group	P 65

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		2007-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.93, 0.95370	ESRF	ID23-1

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	2.1	50	99.9	0.078	0.078	12.6	10.5		10026		3	37.6

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	2.1	2.15	98.5		0.372	0.372		9.3

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 (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 2YUE	2.1	38.66	9516	480	99.9	0.166	0.163	0.1667	0.231	0.2336	RANDOM	40.98

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]
-0.04	-0.02		-0.04		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.075
r_dihedral_angle_4_deg	18.399
r_dihedral_angle_3_deg	14.02
r_dihedral_angle_1_deg	6.914
r_scangle_it	5.566
r_mcangle_it	4.465
r_scbond_it	3.921
r_mcbond_it	3.55
r_angle_refined_deg	1.455
r_symmetry_hbond_refined	0.444
r_nbtor_refined	0.313
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.101
r_metal_ion_refined	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1223
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling