8D5N | pdb_00008d5n

Crystal structure of Ld-HF10

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LD9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH5.5, and 1M Lithium sulfate monohydrate

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.503	α = 90
b = 139.816	β = 130.824
c = 87.344	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 PILATUS3 S 6M		2016-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	77	99.6	0.05	9.6	3.4		102152			31.23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.864			0.738

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1LD9	1.8	50.005	100636	5081	98.798	0.18	0.1777	0.19	0.2186	0.22	39.482

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]
-0.458		0.343	-0.981		0.339

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.47
r_dihedral_angle_4_deg	18.826
r_dihedral_angle_3_deg	16.391
r_lrange_it	8.345
r_lrange_other	8.345
r_dihedral_angle_1_deg	7.594
r_scangle_it	6.564
r_scangle_other	6.564
r_scbond_it	4.375
r_scbond_other	4.375
r_mcangle_it	4.215
r_mcangle_other	4.215
r_mcbond_it	3.047
r_mcbond_other	3.046
r_angle_refined_deg	2.08
r_angle_other_deg	1.542
r_symmetry_nbd_refined	0.302
r_nbd_refined	0.217
r_symmetry_nbd_other	0.203
r_nbd_other	0.186
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.159
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6240
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing