7VIT | pdb_00007vit

Crystal structure of Au(400EQ)-apo-R168H/L169C-rHLFr

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	Ammonium Sulfate, Cadmium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.889	α = 90
b = 180.889	β = 90
c = 180.889	γ = 90

Symmetry
Space Group	F 4 3 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	RIGAKU HyPix-6000HE		2021-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-X	1.540562

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	1.9	12.957	99.7	0.142	0.149	0.046	0.996	17.7	10.2		20431

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	1.9	1.94	100		0.651	0.698	0.249	0.874	3.2

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	1dat	1.9	12.957	19840	1038	96.362	0.185	0.1831	0.17	0.217	0.2	17.355

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.32
r_dihedral_angle_4_deg	20.656
r_dihedral_angle_3_deg	14.115
r_lrange_it	6.492
r_dihedral_angle_1_deg	5.28
r_scangle_it	3.815
r_scbond_it	2.52
r_mcangle_it	2.239
r_angle_refined_deg	1.678
r_mcbond_it	1.432
r_nbtor_refined	0.309
r_symmetry_xyhbond_nbd_refined	0.267
r_xyhbond_nbd_refined	0.266
r_symmetry_nbd_refined	0.26
r_symmetry_metal_ion_refined	0.237
r_nbd_refined	0.223
r_metal_ion_refined	0.133
r_chiral_restr	0.109
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1362
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	23

Software

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