6LOG | pdb_00006log

Crystal structure of human CCL5-12AAA14 mutant

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	283	0.2M Magnesium acetate tetrahydrate pH 7.9, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.329	α = 90
b = 48.329	β = 90
c = 60.401	γ = 120

Symmetry
Space Group	P 31 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	RAYONIX MX300-HS		2019-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.99984	NSRRC	TPS 05A

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	2.44	30	99.7	0.068	0.078	0.036	0.954	20.2	5.5		3262

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	2.44	2.53			0.775	0.861	0.367	0.816	2.6

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	1EQT	2.55	18.88	2749	103	99.2	0.2153	0.2141	0.2198	0.2487	0.27	RANDOM	83.06

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]
1.2	0.6		1.2		-3.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.131
r_dihedral_angle_3_deg	21.425
r_dihedral_angle_4_deg	14.716
r_dihedral_angle_1_deg	9.139
r_angle_refined_deg	2.228
r_angle_other_deg	1.291
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	501
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-2000	data collection
HKL-2000	data reduction