7L5K | pdb_00007l5k

Crystal structure of the DiB-RM protein

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294	2 M ammonium sulfate, 2.5% 2-propanol, 5% w/v n-Dodecyl-b-D-maltoside

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.256	α = 90
b = 69.256	β = 90
c = 80.156	γ = 120

Symmetry
Space Group	P 31

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	MARMOSAIC 225 mm CCD		2017-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	33.32	99.8	0.077	0.036	9.1	4.1		36055			35.517

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	98.7		0.469	0.226	2	3.9

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1QWD	1.86	33.32	34256	1763	99.74	0.1823	0.1803	0.2224	0.2596	RANDOM	38.022

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]
0.28	0.14		0.28		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.036
r_dihedral_angle_4_deg	15.007
r_dihedral_angle_3_deg	12.056
r_dihedral_angle_1_deg	7.523
r_mcangle_it	3.803
r_mcbond_it	3.048
r_mcbond_other	3.048
r_angle_other_deg	2.304
r_angle_refined_deg	1.638
r_chiral_restr	0.08
r_bond_other_d	0.034
r_gen_planes_other	0.016
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2528
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction