5OFS | pdb_00005ofs

X-ray structure of a zinc binding GB1 mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	70% MPD, 100 mM ZnSO4, 100 mM NaCI

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.452	α = 90
b = 75.621	β = 90
c = 51.153	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2016-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.1	42.37	94.6	0.077	0.997	9.35	3.47	213389	739647

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.17	68.7		0.788	0.811	1.35	2.28	57166

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	1IGD	1.1	42.37	106704	5615	95.98	0.12645	0.12547	0.13	0.14501	0.15	RANDOM	16.87

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]
-1.13			-0.37		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.094
r_sphericity_free	30.902
r_sphericity_bonded	15.671
r_dihedral_angle_3_deg	12.348
r_rigid_bond_restr	6.61
r_dihedral_angle_1_deg	6.527
r_long_range_B_refined	4.053
r_long_range_B_other	4.053
r_scangle_other	3.394
r_scbond_it	3.033
r_scbond_other	3.031
r_mcangle_it	2.552
r_mcangle_other	2.551
r_mcbond_it	2.003
r_mcbond_other	1.933
r_angle_refined_deg	1.389
r_angle_other_deg	0.702
r_chiral_restr	0.153
r_bond_refined_d	0.034
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_4_deg
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1800
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	69

Software

Software
Software Name	Purpose
REFMAC	refinement
ADDREF	data reduction
Aimless	data scaling
REFMAC	phasing