2P57 | pdb_00002p57

GAP domain of ZNF289, an ID1-regulated zinc finger protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CRW	pdb entry 2CRW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	3.2M sodium formate, .09M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.027	α = 90
b = 41.165	β = 90
c = 72.808	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	IMAGE PLATE	RIGAKU RAXIS		2006-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	1.8	50	97.8	0.06	15.9	5.4		11721

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)
	1.8	1.86		95.2	0.504		5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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	pdb entry 2CRW	1.8	30	11690	559	97.914	0.198	0.19773	0.1955	0.2	0.2414	0.24	random	18.218

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]
0.699			0.036		-0.735

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.391
r_dihedral_angle_4_deg	21.185
r_dihedral_angle_3_deg	12.627
r_dihedral_angle_1_deg	5.563
r_scangle_it	3.559
r_scbond_it	2.383
r_mcangle_it	1.694
r_angle_refined_deg	1.371
r_mcbond_it	1.121
r_angle_other_deg	0.998
r_symmetry_vdw_other	0.324
r_mcbond_other	0.272
r_nbd_refined	0.215
r_nbd_other	0.192
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.141
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.092
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	981
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
Coot	model building
MolProbity	model building