26QZ | pdb_000026qz

Crystal structure of Rhodostomin ARGDP mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RQG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% PEG4000, 0.2M Ammonium sulfate, 5% PEG3350, 2% PEG200, 0.5% 2-propanol(External) , pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.619	α = 106.839
b = 42.637	β = 103.858
c = 46.538	γ = 97.232

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 210		2013-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.97622	NSRRC	BL13C1

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	30	96.7	0.059	23.9	3.7		19633

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	1.8	1.86			0.459

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.804	23.581	19631	961	96.481	0.161	0.157	0.1692	0.2332	0.2439	35.167

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]
1.327	0.031	1.39	-1.102	-0.61	-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.818
r_dihedral_angle_3_deg	15.621
r_dihedral_angle_4_deg	12.739
r_dihedral_angle_1_deg	7.196
r_scangle_it	6.767
r_scangle_other	6.307
r_lrange_other	6.303
r_lrange_it	6.298
r_scbond_it	5.635
r_scbond_other	5.239
r_mcangle_other	4.743
r_mcangle_it	4.741
r_mcbond_it	3.984
r_mcbond_other	3.98
r_rigid_bond_restr	2.606
r_angle_refined_deg	1.476
r_angle_other_deg	1.316
r_symmetry_nbd_refined	0.277
r_nbd_other	0.219
r_symmetry_nbd_other	0.2
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.187
r_xyhbond_nbd_other	0.162
r_xyhbond_nbd_refined	0.155
r_nbtor_refined	0.152
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1893
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing