5O7K | pdb_00005o7k

Crystal structure of a single chain monellin mutant (Y65R) pH 2.0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	2	293	33% PEG4000, 0.2 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.912	α = 90
b = 31.501	β = 106.24
c = 45.743	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	RIGAKU SATURN 944	MIRRORS	2015-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

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	2.05	30	99.3	0.131	9.55	4.1		11277

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.18	98		0.674	0.847

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	2O9U	2.05	61.88	10651	626	99.42	0.19637	0.19299	0.2	0.25241	0.25	RANDOM	30.078

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]
0.69		-0.15	1.12		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.268
r_dihedral_angle_4_deg	19.289
r_dihedral_angle_3_deg	16.35
r_dihedral_angle_1_deg	7.567
r_long_range_B_refined	5.167
r_long_range_B_other	5.141
r_scangle_other	2.431
r_mcangle_it	2.316
r_mcangle_other	2.315
r_angle_refined_deg	1.958
r_scbond_it	1.521
r_scbond_other	1.489
r_mcbond_it	1.384
r_mcbond_other	1.384
r_angle_other_deg	1.042
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1521
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing