5YSM | pdb_00005ysm

Crystal Structure Analysis of Rif16

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	Magnesium chloride hexahydrate, PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.105	α = 90
b = 70.335	β = 94.43
c = 81.019	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315	mirrors	2017-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.976	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	50	94.1	0.067	0.073	0.028	9	6.3		33798

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	1.8	1.83	90.6		0.475	0.519	0.206	0.895		6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.9	40.42	28027	1459	94.74	0.1857	0.1831	0.192	0.2339	0.2371	RANDOM	22.621

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]
-0.08		0.22	-0.18		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.889
r_dihedral_angle_4_deg	20.643
r_dihedral_angle_3_deg	15.757
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.95
r_angle_other_deg	0.945
r_chiral_restr	0.126
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2794
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing