7VIP | pdb_00007vip

Crystal structure of Au(10EQ)-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
3.17	61.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.126	α = 90
b = 182.126	β = 90
c = 182.126	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)	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	12.882	99.7	0.038	0.013	1	50.6	9.5		20892

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	100		0.145	0.058	0.988	12.2

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	12.882	20873	1054	99.443	0.182	0.1807	0.17	0.2117	0.2	12.442

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	33.271
r_dihedral_angle_4_deg	22.167
r_dihedral_angle_3_deg	13.485
r_lrange_it	6.229
r_dihedral_angle_1_deg	5.502
r_scangle_it	3.901
r_scbond_it	2.577
r_mcangle_it	2.442
r_angle_refined_deg	1.825
r_mcbond_it	1.506
r_metal_ion_refined	0.57
r_symmetry_metal_ion_refined	0.57
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.162
r_chiral_restr	0.107
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1368
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	22

Software

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