7X4V

Crystal structure of Rhodostomin ARGDDP 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	0.2 M NH4OAc, 0.05 M Sodium cacodylate pH 6.5, 30% PEG 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.293	α = 90
b = 62.092	β = 105.61
c = 34.756	γ = 90

Symmetry
Space Group	C 1 2 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		2013-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.00000	SPring-8	BL12B2

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	1.38	30	97.1	0.117	13.4	4.1		32038

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	1.38	1.43			0.55

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	4RQG	1.38	18.09	30379	1658	97.03	0.18469	0.18295	0.21689	RANDOM	15.221

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]
1.22		-0.26	1.13		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.792
r_dihedral_angle_4_deg	15.417
r_dihedral_angle_3_deg	13.704
r_dihedral_angle_1_deg	7.16
r_scangle_other	3.278
r_long_range_B_refined	3.112
r_long_range_B_other	2.965
r_rigid_bond_restr	2.695
r_scbond_other	2.678
r_scbond_it	2.676
r_mcangle_it	2.033
r_mcangle_other	2.031
r_mcbond_other	1.851
r_mcbond_it	1.85
r_angle_other_deg	1.464
r_angle_refined_deg	1.444
r_chiral_restr	0.081
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	950
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms

Software

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