4DXB | pdb_00004dxb

2.29A structure of the engineered MBP TEM-1 fusion protein RG13 in complex with zinc, P1 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZG4	PDB ENTRIES 1ZG4 AND 1OMP
experimental model	PDB	1OMP	PDB ENTRIES 1ZG4 AND 1OMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) and equilibrated over a 1 ml reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.316	α = 83.54
b = 74.177	β = 77.64
c = 103.13	γ = 89.98

Symmetry
Space Group	P 1

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	mirrors	2007-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0810	NSLS	X29A

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	2.29	31.45	56.8	0.054		1.9	62117	59138		1	38.4

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	2.29	2.38	95.5		0.223	3.8	1.9	5876

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1ZG4 AND 1OMP	2.29	31.45	59138	56130	3008	95.2	0.23492	0.23183	0.29166	0.2899	RANDOM	34.401

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		-0.01	-0.01	0.01	0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.971
r_dihedral_angle_3_deg	15.174
r_dihedral_angle_4_deg	12.709
r_dihedral_angle_1_deg	4.515
r_mcangle_it	2.551
r_scangle_it	2.253
r_mcbond_it	1.605
r_scbond_it	1.505
r_angle_refined_deg	0.96
r_nbtor_refined	0.293
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.149
r_xyhbond_nbd_refined	0.112
r_symmetry_hbond_refined	0.097
r_metal_ion_refined	0.07
r_symmetry_metal_ion_refined	0.064
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9834
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	4

Software

Software
Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing