8R4M | pdb_00008r4m

CSP1 M48L mutant with Iodide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5FJD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M Tris-Bicine pH 8.5 plus 12.5% v/v 2-methyl-2,4 pentanediol (racemic), 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 0.03 M sodium fluoride, 0.03 M sodium bromide and 0.03 M sodium iodide

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.744	α = 90
b = 87.744	β = 90
c = 50.15	γ = 90

Symmetry
Space Group	P 42 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 6M		2017-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	43.9	100	0.999	12	13.3		14827

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2			1.736	1.872	0.695	0.793		13.5

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	1.95	43.872	14751	715	99.709	0.181	0.1786	0.1787	0.2297	0.2301	46.818

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]
-2.304			-2.304		4.609

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.708
r_dihedral_angle_4_deg	24.517
r_dihedral_angle_3_deg	15.549
r_lrange_it	7.923
r_scangle_it	7.567
r_scbond_it	5.544
r_mcangle_it	5.144
r_dihedral_angle_1_deg	4.8
r_mcbond_it	4.018
r_angle_refined_deg	1.511
r_nbtor_refined	0.301
r_nbd_refined	0.233
r_symmetry_nbd_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.118
r_ncsr_local_group_1	0.092
r_metal_ion_refined	0.037
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1487
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
XDS	data reduction
MOLREP	phasing
BUSTER	refinement
Coot	model building