8R4L | pdb_00008r4l

CSP1 M48L mutant without 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 14% v/v 2-methyl-2,4 pentanediol (racemic), 14% w/v PEG 1000, 14% w/v PEG 3350, 0.03 M MgCl2 and 0.03 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.579	α = 90
b = 41.755	β = 95.588
c = 53.739	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	PIXEL	DECTRIS PILATUS 6M		2018-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2	38.17	99	0.117	0.16	0.108	0.989	6.7	3.2		14161

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.328		2.7

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	2	38.168	14161	671	98.91	0.223	0.2202	0.2203	0.2706	0.2703	39.092

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]
0.728		0.013	-1.536		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.775
r_dihedral_angle_6_deg	14.616
r_dihedral_angle_2_deg	11.955
r_lrange_other	9.155
r_lrange_it	9.15
r_scangle_it	7.693
r_scangle_other	7.689
r_mcangle_it	5.382
r_mcangle_other	5.382
r_dihedral_angle_1_deg	5.304
r_scbond_other	5.048
r_scbond_it	5.047
r_mcbond_it	3.471
r_mcbond_other	3.47
r_angle_refined_deg	1.616
r_angle_other_deg	0.552
r_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.211
r_metal_ion_refined	0.204
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.158
r_nbd_other	0.145
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_1	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1576
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	27

Software

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